Diff of the two buildlogs: -- --- b1/build.log 2025-08-25 18:20:22.266103294 +0000 +++ b2/build.log 2025-08-25 18:40:12.043520754 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Sep 27 12:36:03 -12 2026 -I: pbuilder-time-stamp: 1790555763 +I: Current time: Tue Aug 26 08:20:25 +14 2025 +I: pbuilder-time-stamp: 1756146025 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying c23.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3100232/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/968878/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 25 18:20 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/968878/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/968878/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='54a1b2ace53d4fc8a6e67cabf7e33503' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3100232' - PS1='# ' - PS2='> ' + INVOCATION_ID=1d255acb815a414fb88b06f8fbc88ffd + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=968878 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AbJsti5a/pbuilderrc_XCuB --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AbJsti5a/b1 --logfile b1/build.log gmap_2024-11-20+ds-2.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AbJsti5a/pbuilderrc_4jQm --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AbJsti5a/b2 --logfile b2/build.log gmap_2024-11-20+ds-2.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3100232/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/968878/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -156,7 +188,7 @@ Get: 33 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 12.8 MB in 1s (8987 kB/s) +Fetched 12.8 MB in 0s (53.1 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19855 files and directories currently installed.) @@ -311,7 +343,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gmap-2024-11-20+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gmap_2024-11-20+ds-2_source.changes +I: user script /srv/workspace/pbuilder/968878/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/968878/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gmap-2024-11-20+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gmap_2024-11-20+ds-2_source.changes dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2024-11-20+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -1806,7 +1842,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_build - cd build && make -j42 + cd build && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' @@ -1850,36 +1886,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -1887,14 +1899,20 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); @@ -1910,15 +1928,16 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -1926,7 +1945,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -1935,8 +1953,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -1959,13 +1975,18 @@ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1975,6 +1996,7 @@ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1987,14 +2009,22 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2094,10 +2124,13 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -2148,117 +2181,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -../../src/iit-read.c: In function 'IIT_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2335,7 +2262,7 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -2359,42 +2286,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -2406,6 +2300,18 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -2455,7 +2361,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -2484,7 +2389,29 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -2495,14 +2422,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -2519,19 +2438,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -2542,7 +2448,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -2589,6 +2494,7 @@ | ~ | | | Oligospace_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -2615,7 +2521,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -2689,6 +2594,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -2725,7 +2631,99 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ @@ -2739,7 +2737,25 @@ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -2751,24 +2767,30 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2906,6 +2928,20 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -2916,26 +2952,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -2948,14 +2964,34 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -2963,11 +2999,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -3018,10 +3049,164 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -3032,7 +3217,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -3075,6 +3259,7 @@ | | | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -3142,6 +3327,7 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -3214,51 +3400,12 @@ | ~ | | | Oligospace_T {aka long unsigned int} -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -3269,36 +3416,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -3309,67 +3426,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3385,7 +3441,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -3476,34 +3531,38 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -3531,32 +3590,11 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -3573,16 +3611,15 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -3633,7 +3670,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c @@ -3645,8 +3681,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); @@ -3655,7 +3689,8 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -3669,6 +3704,7 @@ 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -3685,6 +3721,7 @@ 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ @@ -3696,7 +3733,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -3707,6 +3743,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -3757,13 +3795,29 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3778,6 +3832,7 @@ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3857,66 +3912,21 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -3924,10 +3934,18 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3940,10 +3958,14 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3966,6 +3988,14 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -3994,6 +4024,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -4014,12 +4045,15 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -4070,14 +4104,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4164,6 +4192,7 @@ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4177,28 +4206,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4207,6 +4218,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -4284,6 +4296,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -4298,13 +4311,18 @@ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -4317,7 +4335,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -4326,13 +4343,34 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -4383,13 +4421,32 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4489,34 +4546,12 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -4544,15 +4579,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -4579,6 +4605,8 @@ | | | long long unsigned int | %lu +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -4599,6 +4627,12 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -4635,13 +4669,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -4653,41 +4680,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -4708,19 +4706,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -4731,40 +4716,19 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -4785,6 +4749,22 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -4795,13 +4775,19 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -4818,6 +4804,8 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read.c: In function 'read_words': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -4828,6 +4816,54 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -4842,10 +4878,10 @@ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -4860,6 +4896,10 @@ | | | | long long unsigned int long unsigned int | %lu +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -4871,15 +4911,30 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -4888,6 +4943,7 @@ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -4900,8 +4956,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -4913,34 +4967,12 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4990,35 +5022,59 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5051,6 +5107,19 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -5088,6 +5157,34 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -5111,6 +5208,7 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -5118,18 +5216,50 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -5147,13 +5277,6 @@ | | | long long unsigned int | %lu -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5164,19 +5287,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5187,9 +5297,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5200,19 +5307,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5229,19 +5323,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5268,16 +5349,6 @@ | | | long long unsigned int | %lu -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5288,24 +5359,6 @@ | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5327,13 +5380,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5360,19 +5406,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -5409,6 +5442,14 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -5445,19 +5486,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ @@ -5475,13 +5503,25 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5490,10 +5530,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -5501,6 +5537,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -5517,19 +5555,14 @@ ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -5546,10 +5579,15 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -5582,7 +5620,6 @@ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5601,9 +5638,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -5618,7 +5652,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5627,9 +5660,19 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5704,7 +5747,13 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -5728,23 +5777,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -5787,7 +5819,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -5836,6 +5867,39 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -6058,44 +6122,12 @@ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -6107,13 +6139,15 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -6153,6 +6187,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c @@ -6161,6 +6197,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -6211,76 +6249,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6293,9 +6269,6 @@ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6314,15 +6287,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -6336,9 +6300,6 @@ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6363,13 +6324,8 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6377,6 +6333,22 @@ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} +../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6399,45 +6371,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} -../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -6639,9 +6573,111 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c @@ -6669,8 +6705,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -6690,10 +6724,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -6713,11 +6745,16 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -6768,20 +6805,15 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6813,7 +6845,6 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6864,8 +6895,6 @@ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6875,12 +6904,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -6888,6 +6911,29 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -6899,20 +6945,12 @@ ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6932,6 +6970,7 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -6993,9 +7032,13 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -7007,13 +7050,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c @@ -7060,6 +7096,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -7067,7 +7104,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -7077,6 +7113,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -7096,9 +7133,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -7118,16 +7153,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -7163,7 +7191,6 @@ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -7179,111 +7206,19 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7369,7 +7304,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -7378,7 +7312,6 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': -../../src/compress-write.c: In function 'put_compressed_one': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -7391,6 +7324,106 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ @@ -7404,6 +7437,7 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7412,11 +7446,10 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -7428,7 +7461,13 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -7436,9 +7475,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c @@ -7484,6 +7520,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -7491,7 +7528,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -7501,6 +7537,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -7520,9 +7559,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -7535,6 +7571,7 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -7543,14 +7580,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -7601,10 +7635,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7704,9 +7735,33 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7792,7 +7847,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -7813,24 +7867,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c @@ -7844,14 +7880,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c @@ -7898,9 +7934,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -7909,6 +7942,9 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c @@ -7949,10 +7985,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -7960,6 +7992,10 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c @@ -7991,8 +8027,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -8012,7 +8046,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -8025,7 +8062,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -8042,7 +8078,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -8050,6 +8085,7 @@ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -8096,6 +8132,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -8189,16 +8226,34 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -8207,7 +8262,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -8245,7 +8299,6 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -8286,7 +8339,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -8307,22 +8359,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c @@ -8338,8 +8374,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -8347,6 +8381,8 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c @@ -8372,6 +8408,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -8380,11 +8421,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c @@ -8392,14 +8428,16 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -8421,8 +8459,15 @@ | ~~~~~~~~~~~~~ | | | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c ../../src/path.c: In function 'Path_print': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ @@ -8449,20 +8494,11 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c @@ -8553,7 +8589,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -8561,15 +8596,13 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -8589,35 +8622,18 @@ | | | unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -8663,13 +8679,32 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -8720,16 +8755,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -8806,7 +8833,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -8830,20 +8856,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -8929,6 +8944,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -8949,9 +8965,24 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -8967,6 +8998,11 @@ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c @@ -9004,9 +9040,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -9014,6 +9047,9 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -9028,6 +9064,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -9040,7 +9079,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -9049,31 +9087,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +../../src/littleendian.c: In function 'Littleendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -9124,17 +9143,27 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -9232,33 +9261,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -9274,6 +9276,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -9297,6 +9300,7 @@ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -9351,7 +9355,8 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -9365,31 +9370,62 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -../../src/indexdb.c: In function 'positions_read_multiple_large': In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c @@ -9433,7 +9469,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -9441,6 +9476,7 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -9455,7 +9491,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -9475,6 +9510,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -9498,12 +9534,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -9553,10 +9584,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -9656,26 +9685,14 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -9727,6 +9744,7 @@ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -9781,6 +9799,24 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c @@ -9797,11 +9833,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c @@ -9847,6 +9883,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -9855,13 +9898,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c @@ -9902,11 +9938,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -9914,17 +9945,14 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -9945,8 +9973,13 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -9966,6 +9999,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -9986,6 +10021,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -9993,11 +10029,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -10048,10 +10079,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -10084,7 +10119,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -10098,6 +10132,7 @@ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -10129,7 +10164,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -10153,7 +10187,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -10168,11 +10205,8 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -10182,6 +10216,7 @@ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -10258,7 +10293,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -10266,7 +10300,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -10280,6 +10313,9 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c @@ -10293,6 +10329,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -10300,8 +10338,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c @@ -10327,7 +10363,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -10336,6 +10371,7 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c @@ -10347,27 +10383,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -10395,13 +10412,35 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -10410,9 +10449,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c @@ -10448,6 +10484,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -10489,23 +10530,14 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -10513,12 +10545,10 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -10539,6 +10569,11 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -10558,13 +10593,14 @@ | | | unsigned int | %lu -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm @@ -10590,41 +10626,41 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build -cp gmap_cat.pl gmap_cat -cp md_coords.pl md_coords -cp fa_coords.pl fa_coords -cp psl_splicesites.pl psl_splicesites -cp psl_introns.pl psl_introns -cp psl_genes.pl psl_genes chmod +x gmap_process chmod +x gmap_build +cp gmap_cat.pl gmap_cat +cp md_coords.pl md_coords chmod +x gmap_cat chmod +x md_coords +cp fa_coords.pl fa_coords +cp psl_splicesites.pl psl_splicesites chmod +x fa_coords +cp psl_introns.pl psl_introns chmod +x psl_splicesites chmod +x psl_introns +cp psl_genes.pl psl_genes chmod +x psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites +chmod +x ensembl_genes cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes -cp gtf_transcript_splicesites.pl gtf_transcript_splicesites -cp gff3_splicesites.pl gff3_splicesites -cp gff3_introns.pl gff3_introns -chmod +x ensembl_genes -cp gff3_genes.pl gff3_genes chmod +x gtf_splicesites chmod +x gtf_introns chmod +x gtf_genes -cp dbsnp_iit.pl dbsnp_iit +cp gtf_transcript_splicesites.pl gtf_transcript_splicesites +cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites +cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites -chmod +x gff3_introns +cp gff3_genes.pl gff3_genes +cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit +chmod +x gff3_introns chmod +x gff3_genes -cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x gvf_iit +cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making all in tests @@ -10636,7 +10672,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' dh_auto_build --builddir build_ssse3 - cd build_ssse3 && make -j42 + cd build_ssse3 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' @@ -10674,17 +10710,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -10704,10 +10729,19 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -10716,7 +10750,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -10725,10 +10758,113 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); @@ -10744,6 +10880,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -10756,7 +10893,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -10765,7 +10901,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -10793,7 +10928,6 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -10818,6 +10952,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c @@ -10828,6 +10963,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -10853,7 +10989,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -10879,8 +11014,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -10936,6 +11077,8 @@ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -10948,6 +11091,12 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -10978,15 +11127,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -10998,6 +11138,7 @@ ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11036,7 +11177,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -11066,6 +11206,22 @@ 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': +../../src/compress-write.c: In function 'put_compressed_one': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11085,126 +11241,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -11224,18 +11260,34 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/iit-read.c: In function 'IIT_read': +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11249,6 +11301,16 @@ 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': +../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~~~~~~~~~~~~ + | | + | UINT8 {aka long unsigned int} ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11268,100 +11330,6 @@ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} -../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu -../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11372,6 +11340,12 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11418,6 +11392,19 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11455,6 +11442,22 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11497,6 +11500,7 @@ | | | long long unsigned int | %lu +../../src/iit-read.c: In function 'IIT_debug': ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -11527,6 +11531,13 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -11553,8 +11564,18 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -11569,9 +11590,7 @@ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -11582,9 +11601,16 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -11596,8 +11622,20 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -11661,7 +11699,6 @@ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11736,7 +11773,6 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -11744,11 +11780,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -11768,6 +11799,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -11788,12 +11820,15 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11843,6 +11878,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c @@ -11851,108 +11887,112 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -11964,13 +12004,14 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -12053,6 +12094,36 @@ | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -12063,7 +12134,67 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -12090,6 +12221,13 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -12172,124 +12310,19 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': +../../src/compress-write.c: In function 'put_compressed_one': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -12297,6 +12330,15 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ @@ -12310,14 +12352,7 @@ | | | | long long unsigned int long unsigned int | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -12329,14 +12364,10 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -12364,14 +12395,17 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); @@ -12380,6 +12414,9 @@ ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); @@ -12387,12 +12424,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -12409,6 +12440,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c @@ -12416,9 +12452,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -12469,6 +12502,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -12477,17 +12513,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/iit_store.c: In function 'parse_fasta': -../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 689 | fprintf(stderr,"Assigning %llu to end\n",end); - | ~~~^ ~~~ - | | | - | | Univcoord_T {aka long unsigned int} - | long long unsigned int - | %lu ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -12527,6 +12552,17 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/iit_store.c: In function 'parse_fasta': +../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 689 | fprintf(stderr,"Assigning %llu to end\n",end); + | ~~~^ ~~~ + | | | + | | Univcoord_T {aka long unsigned int} + | long long unsigned int + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -12534,8 +12570,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -12546,6 +12580,7 @@ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12586,12 +12621,12 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -12625,6 +12660,14 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12661,13 +12704,24 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -12691,30 +12745,12 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -12732,12 +12768,8 @@ 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12821,6 +12853,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -12841,6 +12874,9 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -12851,9 +12887,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12879,6 +12913,7 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12903,11 +12938,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12975,7 +13009,6 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -12999,7 +13032,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -13007,10 +13039,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13019,33 +13051,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -13053,22 +13058,10 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13095,7 +13088,6 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13156,6 +13148,50 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -13163,7 +13199,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13227,6 +13268,7 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13235,15 +13277,8 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13274,7 +13309,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -13342,116 +13376,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -13644,10 +13572,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -13664,6 +13588,7 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -13689,7 +13614,6 @@ | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -13700,6 +13624,118 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -13733,7 +13769,9 @@ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -13749,8 +13787,13 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -13762,94 +13805,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13949,8 +13904,85 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13959,6 +13991,107 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -13995,13 +14128,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14038,10 +14164,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14052,18 +14174,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14080,7 +14190,6 @@ | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_intervals': ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14091,32 +14200,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14143,13 +14227,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14160,27 +14237,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -14207,7 +14263,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -14218,12 +14273,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -14234,19 +14283,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -14274,11 +14310,6 @@ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -14304,15 +14335,17 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -14324,6 +14357,9 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -14354,11 +14390,11 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -14371,15 +14407,16 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -14405,6 +14442,7 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -14430,10 +14468,34 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -14533,139 +14595,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -14677,6 +14606,8 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14693,6 +14624,7 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14703,6 +14635,10 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14822,7 +14758,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -14885,6 +14820,113 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -14899,10 +14941,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -14914,17 +14952,10 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -14936,12 +14967,16 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -14961,10 +14996,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -14985,6 +15020,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c @@ -15044,7 +15080,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -15144,114 +15179,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -15279,7 +15206,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -15373,6 +15299,14 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -15415,6 +15349,7 @@ | | | long long unsigned int | %lu +../../src/iit-read.c: In function 'IIT_read': ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -15425,6 +15360,12 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -15435,7 +15376,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +../../src/iit-read.c: In function 'read_tree': ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -15446,12 +15387,41 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -15462,6 +15432,18 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -15472,9 +15454,59 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -15489,6 +15521,10 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -15498,9 +15534,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -15520,6 +15553,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -15533,6 +15567,7 @@ 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ @@ -15540,14 +15575,10 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -15555,6 +15586,7 @@ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -15598,14 +15630,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -15638,7 +15667,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -15706,6 +15734,14 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': @@ -15716,6 +15752,18 @@ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -15724,7 +15772,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -15732,11 +15779,11 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -15762,7 +15809,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -15776,6 +15822,7 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -15826,22 +15873,11 @@ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c @@ -15885,7 +15921,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -15893,6 +15928,7 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -15906,6 +15942,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -15925,8 +15964,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -15947,12 +15984,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -16003,6 +16036,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c @@ -16010,7 +16046,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -16081,6 +16116,7 @@ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16113,7 +16149,44 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -16145,13 +16218,6 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -16178,13 +16244,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -16233,33 +16292,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -16267,6 +16300,9 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c @@ -16332,6 +16368,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -16351,11 +16390,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -16376,6 +16410,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c @@ -16383,7 +16419,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -16434,12 +16469,34 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16537,23 +16594,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -16659,10 +16699,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c @@ -16676,13 +16712,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c @@ -16714,6 +16750,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c @@ -16734,14 +16778,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c @@ -16793,7 +16829,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -16814,6 +16849,7 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -16843,7 +16879,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -16864,15 +16899,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -16923,14 +16954,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -16963,6 +16986,7 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -17000,6 +17024,7 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -17023,7 +17048,7 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -17031,6 +17056,32 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -17075,6 +17126,7 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -17136,22 +17188,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c @@ -17168,9 +17204,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -17178,6 +17211,9 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c @@ -17201,9 +17237,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -17212,6 +17245,9 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c @@ -17221,6 +17257,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c ../../src/altsplice.c: In function 'Altsplice_print': @@ -17249,7 +17293,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/path.c: In function 'Path_print': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ @@ -17276,6 +17319,7 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c @@ -17285,14 +17329,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c @@ -17324,15 +17360,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -17380,13 +17407,17 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -17394,12 +17425,18 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -17413,6 +17450,7 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ @@ -17425,29 +17463,9 @@ | | | unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -17468,8 +17486,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -17490,6 +17506,26 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -17497,10 +17533,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -17530,7 +17562,6 @@ ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17552,10 +17583,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -17625,7 +17659,6 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -17633,7 +17666,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -17657,14 +17689,21 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -17680,7 +17719,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -17771,21 +17809,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -17797,6 +17822,17 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c @@ -17837,6 +17873,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -17844,8 +17882,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -17857,9 +17893,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -17880,8 +17913,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -17901,14 +17932,14 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -17928,14 +17959,12 @@ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -17961,6 +17990,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c @@ -18056,6 +18092,8 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -18063,12 +18101,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -18172,6 +18204,9 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -18194,11 +18229,14 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -18210,7 +18248,7 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -18218,8 +18256,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c @@ -18263,7 +18299,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -18271,6 +18306,7 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -18284,25 +18320,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -18323,15 +18341,30 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -18382,13 +18415,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -18488,7 +18514,15 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -18503,16 +18537,20 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c: In function 'IIT_read': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -18561,7 +18599,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -18597,6 +18634,7 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -18610,8 +18648,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c @@ -18623,16 +18659,16 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c @@ -18672,9 +18708,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -18683,6 +18716,9 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c @@ -18732,6 +18768,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -18739,16 +18776,7 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -18769,35 +18797,34 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -18810,20 +18837,27 @@ 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -18973,6 +19007,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c @@ -18984,7 +19020,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -19104,6 +19139,7 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c @@ -19120,11 +19156,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -19132,6 +19163,11 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c @@ -19156,7 +19192,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -19165,6 +19200,7 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c @@ -19173,18 +19209,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -19233,6 +19257,10 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c @@ -19252,6 +19280,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c @@ -19335,9 +19371,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -19345,9 +19378,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -19368,6 +19398,24 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -19393,18 +19441,6 @@ | | | unsigned int | %lu -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm @@ -19419,42 +19455,42 @@ Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' cp gmap_process.pl gmap_process +chmod +x gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat +chmod +x gmap_build cp md_coords.pl md_coords +chmod +x gmap_cat cp fa_coords.pl fa_coords +chmod +x md_coords cp psl_splicesites.pl psl_splicesites +chmod +x fa_coords +chmod +x psl_splicesites cp psl_introns.pl psl_introns -chmod +x gmap_process cp psl_genes.pl psl_genes -chmod +x gmap_build cp ensembl_genes.pl ensembl_genes -chmod +x md_coords -chmod +x fa_coords -chmod +x gmap_cat -chmod +x psl_splicesites -chmod +x psl_introns cp gtf_splicesites.pl gtf_splicesites +chmod +x psl_introns chmod +x psl_genes -chmod +x ensembl_genes cp gtf_introns.pl gtf_introns +chmod +x ensembl_genes +chmod +x gtf_splicesites +chmod +x gtf_introns cp gtf_genes.pl gtf_genes +chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites +chmod +x gtf_transcript_splicesites +chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns -chmod +x gtf_splicesites cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit -chmod +x gtf_introns -chmod +x gtf_genes cp gvf_iit.pl gvf_iit -chmod +x gff3_splicesites -cp vcf_iit.pl vcf_iit chmod +x gff3_introns -chmod +x gtf_transcript_splicesites chmod +x gff3_genes chmod +x dbsnp_iit chmod +x gvf_iit +cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' Making all in tests @@ -19466,7 +19502,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_build --builddir build_sse41 - cd build_sse41 && make -j42 + cd build_sse41 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' @@ -19504,57 +19540,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -19574,7 +19559,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -19591,11 +19580,26 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -19612,7 +19616,6 @@ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -19647,14 +19650,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -19725,12 +19720,31 @@ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -19754,70 +19768,27 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'IIT_read': +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -19854,7 +19825,6 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -19895,7 +19865,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -19904,7 +19873,6 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -19917,16 +19885,80 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -20019,14 +20051,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -20034,6 +20058,19 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -20042,8 +20079,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -20080,14 +20115,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -20149,18 +20176,33 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -20323,6 +20365,7 @@ | | | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -20343,6 +20386,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -20369,6 +20413,7 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -20379,28 +20424,26 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -20411,10 +20454,7 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -20426,9 +20466,7 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -20566,8 +20604,6 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c @@ -20577,27 +20613,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -20617,13 +20632,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -20674,6 +20682,34 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c @@ -20682,8 +20718,105 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -20866,75 +20999,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -20945,35 +21009,12 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -20994,15 +21035,11 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ @@ -21017,14 +21054,6 @@ | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -21035,6 +21064,14 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -21112,7 +21149,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -21133,7 +21169,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -21148,22 +21183,22 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -../../src/indexdb.c: In function 'positions_read_multiple': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -21191,6 +21226,7 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c @@ -21198,6 +21234,27 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -21218,36 +21275,10 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -21273,7 +21304,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -21299,14 +21329,18 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); @@ -21315,7 +21349,6 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -21335,7 +21368,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -21344,7 +21378,6 @@ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -21357,6 +21390,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -21364,56 +21400,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -21422,6 +21408,47 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -21521,49 +21548,64 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -21572,7 +21614,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -21610,7 +21651,6 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -21671,15 +21711,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -21730,14 +21761,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -21746,6 +21771,7 @@ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -21837,28 +21863,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -21867,7 +21872,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -21965,7 +21969,18 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -21982,12 +21997,33 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c @@ -21996,6 +22032,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -22046,11 +22083,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -22065,8 +22098,14 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -22137,7 +22176,6 @@ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -22160,8 +22198,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -22169,12 +22205,117 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': @@ -22395,7 +22536,10 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -22410,14 +22554,6 @@ | | | | long long unsigned int long unsigned int | %lu -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -22429,118 +22565,6 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/iit-read.c: In function 'read_tree': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -22552,6 +22576,18 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -22572,9 +22608,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -22594,9 +22628,38 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -22622,7 +22685,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -22648,36 +22710,37 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -22747,13 +22810,26 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read-univ.c: In function 'read_words': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -22770,62 +22846,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -22839,16 +22859,13 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -22862,12 +22879,6 @@ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -22883,6 +22894,82 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} +../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -22893,7 +22980,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -22904,12 +22990,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -22946,7 +23026,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -22957,18 +23036,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -22995,7 +23062,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -23105,42 +23171,11 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -23152,6 +23187,7 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -23161,13 +23197,31 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -23184,25 +23238,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c @@ -23210,9 +23246,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -23263,31 +23296,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -23321,7 +23334,6 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -23388,9 +23400,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -23408,8 +23420,6 @@ | | | long long unsigned int | %lu -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -23420,12 +23430,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -23508,27 +23512,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -23539,28 +23523,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -23571,19 +23539,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -23604,34 +23559,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -23658,13 +23585,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -23691,6 +23611,134 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] + 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5646 | n,n/BLOCKSIZE,totalcount,nextpage); + | ~~~~~~~~ + | | + | UINT8 {aka long unsigned int} +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -23704,16 +23752,16 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] - 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5646 | n,n/BLOCKSIZE,totalcount,nextpage); - | ~~~~~~~~ - | | - | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -23739,22 +23787,6 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -23766,13 +23798,16 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -23792,10 +23827,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -23804,7 +23837,6 @@ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -23817,6 +23849,10 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c @@ -23874,109 +23910,7 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -24194,60 +24128,165 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -../../src/iit-read.c: In function 'IIT_read': +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' @@ -24301,9 +24340,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -24329,7 +24365,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -24369,6 +24404,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -24379,6 +24415,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -24429,11 +24466,123 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -24479,7 +24628,6 @@ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -24534,12 +24682,13 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -24548,129 +24697,16 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c @@ -24715,6 +24751,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -24722,11 +24763,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -24737,6 +24773,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -24756,7 +24793,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -24835,114 +24871,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -24951,7 +24879,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -24988,7 +24915,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -25037,7 +24963,8 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -25051,6 +24978,127 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -25073,22 +25121,16 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -25096,12 +25138,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c @@ -25142,8 +25178,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -25151,6 +25185,8 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c @@ -25162,6 +25198,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -25201,14 +25238,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -25234,7 +25268,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -25260,10 +25293,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -25363,15 +25400,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -25403,20 +25434,6 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -25430,6 +25447,7 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -25471,6 +25489,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -25491,6 +25510,23 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c @@ -25503,11 +25539,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c @@ -25558,6 +25594,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -25566,11 +25607,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c @@ -25610,6 +25646,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -25617,15 +25659,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -25646,12 +25679,19 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -25671,12 +25711,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -25693,14 +25731,17 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -25751,11 +25792,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -25858,28 +25894,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -25888,6 +25902,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -25895,6 +25910,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -25972,6 +25988,7 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -25985,6 +26002,25 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c @@ -25997,13 +26033,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -26011,6 +26040,13 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c @@ -26034,6 +26070,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -26042,12 +26084,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c @@ -26055,6 +26091,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -26076,10 +26121,7 @@ | ~~~~~~~~~~~~~ | | | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -26107,20 +26149,14 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c @@ -26214,6 +26250,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -26221,13 +26261,7 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -26253,11 +26287,12 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -26278,7 +26313,7 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -26298,7 +26333,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -26311,7 +26348,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -26327,8 +26363,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26378,12 +26415,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26481,28 +26520,11 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26516,7 +26538,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -26575,7 +26596,6 @@ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26585,6 +26605,14 @@ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26596,7 +26624,6 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26609,15 +26636,22 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -../../src/indexdb.c: In function 'positions_read_multiple': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26626,9 +26660,11 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c @@ -26669,6 +26705,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -26676,7 +26713,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -26687,6 +26723,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -26706,13 +26751,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -26721,25 +26763,14 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -26790,9 +26821,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -26869,7 +26904,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -26893,8 +26927,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -26911,7 +26943,6 @@ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': -../../src/compress-write.c: In function 'put_compressed_one': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26927,12 +26958,6 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -26959,13 +26984,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -27014,7 +27032,27 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -27023,9 +27061,18 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -27037,20 +27084,9 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -../../src/indexdb.c: In function 'positions_read_multiple_large': -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c @@ -27092,15 +27128,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -27114,7 +27150,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -27154,70 +27189,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -27317,6 +27294,65 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': @@ -27333,7 +27369,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -27424,6 +27459,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: @@ -27495,6 +27531,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c @@ -27508,14 +27552,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c @@ -27562,8 +27598,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -27571,11 +27605,16 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -27596,9 +27635,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c @@ -27606,27 +27642,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -27646,17 +27664,28 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -27682,7 +27711,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -27708,16 +27736,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -27808,7 +27829,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -27816,24 +27836,14 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -27939,6 +27949,32 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c @@ -27951,6 +27987,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -27958,11 +27999,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c @@ -27987,8 +28023,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -../../src/knownindels.c: In function 'Knownindels_new_from_dump': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c +../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ @@ -27996,8 +28034,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c @@ -28007,30 +28043,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -28038,7 +28054,6 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ @@ -28061,8 +28076,32 @@ | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -28071,9 +28110,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c @@ -28113,6 +28149,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -28120,7 +28160,6 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -28161,10 +28200,32 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c +../../src/support.c: In function 'Support_dump': +../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ + | ~^ + | | + | unsigned int + | %lu +../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ + | ~^ + | | + | unsigned int + | %lu +../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ + | ~^ + | | + | unsigned int + | %lu +../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ + | ~^ + | | + | unsigned int + | %lu ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -28181,11 +28242,6 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -28203,40 +28259,20 @@ inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm -../../src/support.c: In function 'Support_dump': -../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ - | ~^ - | | - | unsigned int - | %lu -../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ - | ~^ - | | - | unsigned int - | %lu -../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ - | ~^ - | | - | unsigned int - | %lu -../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ - | ~^ - | | - | unsigned int - | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm @@ -28251,37 +28287,37 @@ cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat +chmod +x gmap_process +chmod +x gmap_build +chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes -chmod +x gmap_process -chmod +x gmap_build -chmod +x gmap_cat chmod +x md_coords -cp ensembl_genes.pl ensembl_genes chmod +x fa_coords +chmod +x psl_genes chmod +x psl_splicesites -cp gtf_splicesites.pl gtf_splicesites chmod +x psl_introns -chmod +x psl_genes +cp ensembl_genes.pl ensembl_genes +cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns -cp gtf_genes.pl gtf_genes chmod +x ensembl_genes -cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_splicesites +chmod +x gtf_introns +cp gtf_genes.pl gtf_genes +cp gtf_transcript_splicesites.pl gtf_transcript_splicesites +chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns -chmod +x gtf_introns +chmod +x gtf_transcript_splicesites +chmod +x gff3_splicesites +chmod +x gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit -chmod +x gtf_genes cp gvf_iit.pl gvf_iit -chmod +x gtf_transcript_splicesites -chmod +x gff3_splicesites cp vcf_iit.pl vcf_iit -chmod +x gff3_introns chmod +x gff3_genes chmod +x dbsnp_iit chmod +x gvf_iit @@ -28296,7 +28332,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_build --builddir build_sse42 - cd build_sse42 && make -j42 + cd build_sse42 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' @@ -28342,49 +28378,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -28424,9 +28417,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -28452,40 +28442,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -28555,14 +28511,21 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -28586,6 +28549,79 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -28637,16 +28673,16 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -28683,7 +28719,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -28697,7 +28732,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -28740,16 +28774,13 @@ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -28819,7 +28850,18 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/iit-read-univ.c: In function 'read_words': +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -28849,34 +28891,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -28921,7 +28936,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -28935,16 +28949,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -28952,6 +28956,7 @@ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -28973,14 +28978,99 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -../../src/iit-read.c: In function 'IIT_debug': ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -28991,23 +29081,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -29018,19 +29091,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -29093,7 +29153,6 @@ | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -29187,7 +29246,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -29214,38 +29272,14 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -29257,9 +29291,8 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -29397,15 +29430,14 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -29425,11 +29457,19 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -29446,15 +29486,12 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -29505,15 +29542,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -29583,7 +29616,6 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -29592,16 +29624,6 @@ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -29617,12 +29639,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -29630,6 +29646,27 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} +../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -29831,15 +29868,40 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -29918,12 +29980,19 @@ 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': +../../src/compress-write.c: In function 'put_compressed_one': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -29937,17 +30006,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/compress-write.c: In function 'put_compressed_one': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -29963,38 +30021,23 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -30015,7 +30058,6 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ @@ -30023,29 +30065,10 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -30066,15 +30089,26 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -30125,6 +30159,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -30138,39 +30174,19 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/iit_store.c: In function 'parse_fasta': -../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 689 | fprintf(stderr,"Assigning %llu to end\n",end); - | ~~~^ ~~~ - | | | - | | Univcoord_T {aka long unsigned int} - | long long unsigned int - | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c -../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -30189,6 +30205,26 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +../../src/iit_store.c: In function 'parse_fasta': +../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 689 | fprintf(stderr,"Assigning %llu to end\n",end); + | ~~~^ ~~~ + | | | + | | Univcoord_T {aka long unsigned int} + | long long unsigned int + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c @@ -30196,7 +30232,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -30222,10 +30257,12 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30247,11 +30284,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -30315,6 +30354,10 @@ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30328,7 +30371,11 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/iit-read-univ.c: In function 'read_annotations': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30344,28 +30391,37 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ @@ -30373,37 +30429,23 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -30453,7 +30495,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -30482,7 +30523,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -30490,7 +30530,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -30504,12 +30543,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -30560,6 +30593,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -30634,6 +30670,7 @@ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30656,18 +30693,19 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read-univ.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -30687,6 +30725,26 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -30695,6 +30753,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -30703,7 +30762,6 @@ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30773,10 +30831,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -30784,8 +30838,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -30793,28 +30845,12 @@ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -30822,10 +30858,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -30876,36 +30908,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -30998,7 +31000,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -31006,6 +31007,148 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +../../src/iit-read.c: In function 'read_tree': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -31079,7 +31222,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -31153,7 +31295,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -31190,6 +31331,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb.c: In function 'positions_read_multiple': ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -31226,7 +31368,9 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -31241,26 +31385,7 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -31271,103 +31396,6 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -31379,6 +31407,20 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -31398,12 +31440,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -31414,7 +31450,6 @@ 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ @@ -31426,13 +31461,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -31483,28 +31512,16 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -31523,12 +31540,6 @@ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -31608,9 +31619,32 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -31619,6 +31653,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -31655,7 +31690,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -31669,17 +31703,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -31708,6 +31731,62 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -31724,13 +31803,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -31751,19 +31823,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -31935,41 +31994,20 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -31981,8 +32019,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c @@ -31990,10 +32026,30 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -32014,26 +32070,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -32041,7 +32077,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -32092,33 +32127,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -32195,7 +32205,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -32219,7 +32228,33 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -32235,7 +32270,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -32266,6 +32300,7 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -32278,6 +32313,17 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -32294,6 +32340,12 @@ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -32303,46 +32355,6 @@ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} -../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -32353,6 +32365,9 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -32409,6 +32424,14 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -32472,6 +32495,18 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -32518,6 +32553,7 @@ | ~ | | | Oligospace_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -32545,6 +32581,12 @@ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -32559,10 +32601,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -32574,8 +32612,6 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c @@ -32583,8 +32619,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -32596,12 +32630,13 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -32621,6 +32656,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': @@ -32649,6 +32685,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -32699,14 +32738,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -32715,6 +32750,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -32751,6 +32787,7 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -32764,7 +32801,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -32784,7 +32820,6 @@ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -32794,6 +32829,29 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -32804,14 +32862,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read.c: In function 'IIT_debug': ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -32822,12 +32878,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -32838,7 +32888,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -32849,18 +32898,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -33032,6 +33069,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33131,14 +33169,12 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -33158,25 +33194,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33186,6 +33203,7 @@ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -33198,7 +33216,25 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -33209,6 +33245,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -33222,7 +33264,6 @@ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -33235,7 +33276,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -33261,9 +33301,15 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33296,7 +33342,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -33341,7 +33386,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -33367,14 +33411,6 @@ | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c @@ -33390,6 +33426,7 @@ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -33486,6 +33523,11 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -33497,12 +33539,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c @@ -33547,7 +33583,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -33555,6 +33590,7 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -33566,15 +33602,27 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); @@ -33586,19 +33634,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -33607,6 +33642,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -33670,8 +33706,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33764,7 +33798,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -33772,8 +33805,12 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33818,6 +33855,7 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -33831,13 +33869,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -33866,13 +33897,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -33880,7 +33904,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -33894,6 +33917,22 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33902,13 +33941,10 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -33920,6 +33956,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -33927,7 +33964,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c @@ -33974,7 +34010,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -33982,6 +34017,7 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -33992,10 +34028,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -34035,10 +34067,15 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -34089,12 +34126,114 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -34194,6 +34333,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c @@ -34214,114 +34355,9 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c @@ -34334,16 +34370,16 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c @@ -34382,14 +34418,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -34398,6 +34426,14 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c @@ -34440,6 +34476,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -34447,18 +34485,12 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -34479,6 +34511,10 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c @@ -34501,6 +34537,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -34521,8 +34559,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -34532,6 +34568,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -34582,13 +34623,20 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -34658,7 +34706,6 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -34689,27 +34736,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -34815,6 +34842,15 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c @@ -34828,8 +34864,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -34837,6 +34871,8 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c @@ -34864,6 +34900,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -34872,9 +34911,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c @@ -34883,33 +34919,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -34937,6 +34946,41 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c @@ -34948,14 +34992,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c @@ -34984,19 +35020,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c ../../src/stage1hr.c: In function 'Stage1_list_extension': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ @@ -35037,15 +35061,28 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -35053,10 +35090,15 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -35082,12 +35124,9 @@ | | | unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -35108,9 +35147,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -35127,6 +35163,10 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -35146,10 +35186,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -35174,20 +35210,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -35238,114 +35260,15 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -35445,6 +35368,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -35456,6 +35381,121 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c @@ -35464,10 +35504,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c @@ -35503,13 +35539,24 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -35528,17 +35575,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -35576,70 +35612,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -35739,6 +35711,11 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -35815,6 +35792,7 @@ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -35844,9 +35822,61 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -35858,9 +35888,11 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -35883,6 +35915,10 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c @@ -35933,11 +35969,17 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -35957,8 +35999,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -35979,13 +36020,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -36005,6 +36041,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -36055,7 +36092,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c @@ -36094,6 +36130,8 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -36101,6 +36139,12 @@ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -36155,25 +36199,13 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -36210,7 +36242,6 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -36271,6 +36302,10 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -36285,6 +36320,11 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c @@ -36298,10 +36338,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c @@ -36325,7 +36361,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c @@ -36336,14 +36380,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c @@ -36400,13 +36436,32 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -36426,9 +36481,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -36449,6 +36501,10 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -36456,33 +36512,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c @@ -36493,6 +36522,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c @@ -36503,65 +36539,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -36661,10 +36638,24 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -36673,6 +36664,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -36681,6 +36673,7 @@ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -36757,7 +36750,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -36771,23 +36763,74 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c @@ -36802,13 +36845,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c -../../src/indexdb.c: In function 'positions_read_multiple_large': -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c @@ -36835,19 +36871,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -36856,19 +36881,9 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c -../../src/path.c: In function 'Path_print': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -36890,6 +36905,10 @@ | ~~~~~~~~~~~~~ | | | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c +../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ @@ -36916,6 +36935,23 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c @@ -36952,8 +36988,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -37001,9 +37035,11 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm @@ -37021,33 +37057,6 @@ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse42 gmap_sse42-except.o gmap_sse42-assert.o gmap_sse42-mem.o gmap_sse42-intlist.o gmap_sse42-uintlist.o gmap_sse42-list.o gmap_sse42-littleendian.o gmap_sse42-bigendian.o gmap_sse42-univinterval.o gmap_sse42-interval.o gmap_sse42-stopwatch.o gmap_sse42-semaphore.o gmap_sse42-access.o gmap_sse42-filestring.o gmap_sse42-iit-read-univ.o gmap_sse42-iit-read.o gmap_sse42-md5.o gmap_sse42-bzip2.o gmap_sse42-fopen.o gmap_sse42-sequence.o gmap_sse42-reader.o gmap_sse42-genomicpos.o gmap_sse42-compress.o gmap_sse42-compress-write.o gmap_sse42-gbuffer.o gmap_sse42-genome.o gmap_sse42-popcount.o gmap_sse42-dinucl_bits.o gmap_sse42-genome_canonical.o gmap_sse42-genome-write.o gmap_sse42-bitpack64-read.o gmap_sse42-bitpack64-readtwo.o gmap_sse42-indexdb.o gmap_sse42-oligo.o gmap_sse42-block.o gmap_sse42-chrom.o gmap_sse42-segmentpos.o gmap_sse42-chrnum.o gmap_sse42-uinttable_rh.o gmap_sse42-gregion.o gmap_sse42-match.o gmap_sse42-matchpool.o gmap_sse42-diagnostic.o gmap_sse42-stage1.o gmap_sse42-diag.o gmap_sse42-diagpool.o gmap_sse42-cmet.o gmap_sse42-atoi.o gmap_sse42-orderstat.o gmap_sse42-oligoindex_hr.o gmap_sse42-intron.o gmap_sse42-maxent.o gmap_sse42-maxent_hr.o gmap_sse42-pair.o gmap_sse42-pairpool.o gmap_sse42-cellpool.o gmap_sse42-stage2.o gmap_sse42-doublelist.o gmap_sse42-smooth.o gmap_sse42-splicestringpool.o gmap_sse42-splicetrie_build.o gmap_sse42-splicetrie.o gmap_sse42-boyer-moore.o gmap_sse42-dynprog.o gmap_sse42-dynprog_simd.o gmap_sse42-dynprog_single.o gmap_sse42-dynprog_genome.o gmap_sse42-dynprog_cdna.o gmap_sse42-dynprog_end.o gmap_sse42-translation.o gmap_sse42-pbinom.o gmap_sse42-changepoint.o gmap_sse42-stage3.o gmap_sse42-request.o gmap_sse42-result.o gmap_sse42-output.o gmap_sse42-inbuffer.o gmap_sse42-samheader.o gmap_sse42-printbuffer.o gmap_sse42-outbuffer.o gmap_sse42-chimera.o gmap_sse42-datadir.o gmap_sse42-parserange.o gmap_sse42-getline.o gmap_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse42 gmapl_sse42-except.o gmapl_sse42-assert.o gmapl_sse42-mem.o gmapl_sse42-intlist.o gmapl_sse42-uintlist.o gmapl_sse42-uint8list.o gmapl_sse42-list.o gmapl_sse42-littleendian.o gmapl_sse42-bigendian.o gmapl_sse42-univinterval.o gmapl_sse42-interval.o gmapl_sse42-stopwatch.o gmapl_sse42-semaphore.o gmapl_sse42-access.o gmapl_sse42-filestring.o gmapl_sse42-iit-read-univ.o gmapl_sse42-iit-read.o gmapl_sse42-md5.o gmapl_sse42-bzip2.o gmapl_sse42-fopen.o gmapl_sse42-sequence.o gmapl_sse42-reader.o gmapl_sse42-genomicpos.o gmapl_sse42-compress.o gmapl_sse42-compress-write.o gmapl_sse42-gbuffer.o gmapl_sse42-genome.o gmapl_sse42-popcount.o gmapl_sse42-dinucl_bits.o gmapl_sse42-genome_canonical.o gmapl_sse42-genome-write.o gmapl_sse42-bitpack64-read.o gmapl_sse42-bitpack64-readtwo.o gmapl_sse42-indexdb.o gmapl_sse42-oligo.o gmapl_sse42-block.o gmapl_sse42-chrom.o gmapl_sse42-segmentpos.o gmapl_sse42-chrnum.o gmapl_sse42-uinttable_rh.o gmapl_sse42-uint8table_rh.o gmapl_sse42-gregion.o gmapl_sse42-match.o gmapl_sse42-matchpool.o gmapl_sse42-diagnostic.o gmapl_sse42-stage1.o gmapl_sse42-diag.o gmapl_sse42-diagpool.o gmapl_sse42-cmet.o gmapl_sse42-atoi.o gmapl_sse42-orderstat.o gmapl_sse42-oligoindex_hr.o gmapl_sse42-intron.o gmapl_sse42-maxent.o gmapl_sse42-maxent_hr.o gmapl_sse42-pair.o gmapl_sse42-pairpool.o gmapl_sse42-cellpool.o gmapl_sse42-stage2.o gmapl_sse42-doublelist.o gmapl_sse42-smooth.o gmapl_sse42-splicestringpool.o gmapl_sse42-splicetrie_build.o gmapl_sse42-splicetrie.o gmapl_sse42-boyer-moore.o gmapl_sse42-dynprog.o gmapl_sse42-dynprog_simd.o gmapl_sse42-dynprog_single.o gmapl_sse42-dynprog_genome.o gmapl_sse42-dynprog_cdna.o gmapl_sse42-dynprog_end.o gmapl_sse42-translation.o gmapl_sse42-pbinom.o gmapl_sse42-changepoint.o gmapl_sse42-stage3.o gmapl_sse42-request.o gmapl_sse42-result.o gmapl_sse42-output.o gmapl_sse42-inbuffer.o gmapl_sse42-samheader.o gmapl_sse42-printbuffer.o gmapl_sse42-outbuffer.o gmapl_sse42-chimera.o gmapl_sse42-datadir.o gmapl_sse42-parserange.o gmapl_sse42-getline.o gmapl_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse42 gsnap_sse42-except.o gsnap_sse42-assert.o gsnap_sse42-mem.o gsnap_sse42-intlist.o gsnap_sse42-uintlist.o gsnap_sse42-list.o gsnap_sse42-littleendian.o gsnap_sse42-bigendian.o gsnap_sse42-univinterval.o gsnap_sse42-interval.o gsnap_sse42-stopwatch.o gsnap_sse42-semaphore.o gsnap_sse42-access.o gsnap_sse42-filestring.o gsnap_sse42-iit-read-univ.o gsnap_sse42-iit-read.o gsnap_sse42-bzip2.o gsnap_sse42-reader.o gsnap_sse42-genomicpos.o gsnap_sse42-compress.o gsnap_sse42-genome.o gsnap_sse42-transcriptome.o gsnap_sse42-popcount.o gsnap_sse42-genomebits.o gsnap_sse42-genomebits_consec.o gsnap_sse42-genomebits_count.o gsnap_sse42-genomebits_kmer.o gsnap_sse42-genomebits_indel.o gsnap_sse42-genomebits_decode.o gsnap_sse42-genomebits_mismatches.o gsnap_sse42-genomebits_trim.o gsnap_sse42-dinucl_bits.o gsnap_sse42-genome_sites.o gsnap_sse42-bitpack64-read.o gsnap_sse42-bitpack64-readtwo.o gsnap_sse42-mergeinfo.o gsnap_sse42-merge-diagonals-heap-uint4.o gsnap_sse42-merge-uint4.o gsnap_sse42-merge-diagonals-simd-uint4.o gsnap_sse42-indexdb.o gsnap_sse42-localdb-read.o gsnap_sse42-oligo.o gsnap_sse42-chrnum.o gsnap_sse42-maxent_hr.o gsnap_sse42-mapq.o gsnap_sse42-fopen.o gsnap_sse42-shortread.o gsnap_sse42-junction.o gsnap_sse42-concordance.o gsnap_sse42-simplepair.o gsnap_sse42-orderstat.o gsnap_sse42-intlistpool.o gsnap_sse42-uintlistpool.o gsnap_sse42-listpool.o gsnap_sse42-hitlistpool.o gsnap_sse42-pathpool.o gsnap_sse42-auxinfopool.o gsnap_sse42-pathstorepool.o gsnap_sse42-intron.o gsnap_sse42-gbuffer.o gsnap_sse42-select64-common.o gsnap_sse42-select64-ones.o gsnap_sse42-select64-zeroes.o gsnap_sse42-ef64.o gsnap_sse42-nr-x.o gsnap_sse42-knownsplicing.o gsnap_sse42-knownindels.o gsnap_sse42-splice.o gsnap_sse42-indel.o gsnap_sse42-spliceendsgen.o gsnap_sse42-spliceends.o gsnap_sse42-bitpack64-access.o gsnap_sse42-trdiag.o gsnap_sse42-trdiagpool.o gsnap_sse42-tr-extension-search.o gsnap_sse42-univdiag.o gsnap_sse42-univdiagpool.o gsnap_sse42-sedgesort.o gsnap_sse42-auxinfo.o gsnap_sse42-pathstore.o gsnap_sse42-altsplice.o gsnap_sse42-path.o gsnap_sse42-pathpair.o gsnap_sse42-path-solve.o gsnap_sse42-path-fusion.o gsnap_sse42-path-trim.o gsnap_sse42-path-eval.o gsnap_sse42-pathpair-eval.o gsnap_sse42-path-print-alignment.o gsnap_sse42-path-print-m8.o gsnap_sse42-path-print-sam.o gsnap_sse42-path-learn.o gsnap_sse42-method.o gsnap_sse42-doublelist.o gsnap_sse42-bitvector.o gsnap_sse42-transcriptpool.o gsnap_sse42-exon.o gsnap_sse42-transcript.o gsnap_sse42-trpathpool.o gsnap_sse42-trpath.o gsnap_sse42-trpath-solve.o gsnap_sse42-trpath-convert.o gsnap_sse42-trpath-eval.o gsnap_sse42-transcriptome-search.o gsnap_sse42-vectorpool.o gsnap_sse42-repair.o gsnap_sse42-transcript-remap.o gsnap_sse42-transcript-velocity.o gsnap_sse42-intersect-small.o gsnap_sse42-intersect-uint2.o gsnap_sse42-intersect-approx-uint4.o gsnap_sse42-intersect-approx-indices-uint4.o gsnap_sse42-intersect-wdups-indices.o gsnap_sse42-intersect-lower-small.o gsnap_sse42-intersect-higher-small.o gsnap_sse42-intersect-indices-small.o gsnap_sse42-intersect-indices2-small.o gsnap_sse42-intersect-concordance-uint4.o gsnap_sse42-kmer-search.o gsnap_sse42-extension-search.o gsnap_sse42-repetitive.o gsnap_sse42-uint8table.o gsnap_sse42-uinttable.o gsnap_sse42-stage1hr.o gsnap_sse42-stage1hr-single.o gsnap_sse42-stage1hr-paired.o gsnap_sse42-uinttableuint.o gsnap_sse42-tableuint.o gsnap_sse42-single-cell.o gsnap_sse42-request.o gsnap_sse42-resulthr.o gsnap_sse42-output.o gsnap_sse42-inbuffer.o gsnap_sse42-samheader.o gsnap_sse42-printbuffer.o gsnap_sse42-outbuffer.o gsnap_sse42-uintpairtable.o gsnap_sse42-splice-count.o gsnap_sse42-support.o gsnap_sse42-datadir.o gsnap_sse42-parserange.o gsnap_sse42-getline.o gsnap_sse42-gsnap.o -lz -lbz2 -lm -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -37073,6 +37082,33 @@ | | | unsigned int | %lu +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse42 gsnapl_sse42-except.o gsnapl_sse42-assert.o gsnapl_sse42-mem.o gsnapl_sse42-intlist.o gsnapl_sse42-uintlist.o gsnapl_sse42-uint8list.o gsnapl_sse42-list.o gsnapl_sse42-littleendian.o gsnapl_sse42-bigendian.o gsnapl_sse42-univinterval.o gsnapl_sse42-interval.o gsnapl_sse42-stopwatch.o gsnapl_sse42-semaphore.o gsnapl_sse42-access.o gsnapl_sse42-filestring.o gsnapl_sse42-iit-read-univ.o gsnapl_sse42-iit-read.o gsnapl_sse42-bzip2.o gsnapl_sse42-reader.o gsnapl_sse42-genomicpos.o gsnapl_sse42-compress.o gsnapl_sse42-genome.o gsnapl_sse42-transcriptome.o gsnapl_sse42-popcount.o gsnapl_sse42-genomebits.o gsnapl_sse42-genomebits_consec.o gsnapl_sse42-genomebits_count.o gsnapl_sse42-genomebits_kmer.o gsnapl_sse42-genomebits_indel.o gsnapl_sse42-genomebits_decode.o gsnapl_sse42-genomebits_mismatches.o gsnapl_sse42-genomebits_trim.o gsnapl_sse42-dinucl_bits.o gsnapl_sse42-genome_sites.o gsnapl_sse42-bitpack64-read.o gsnapl_sse42-bitpack64-readtwo.o gsnapl_sse42-mergeinfo.o gsnapl_sse42-merge-diagonals-heap-uint8.o gsnapl_sse42-merge-uint8.o gsnapl_sse42-merge-diagonals-simd-uint8.o gsnapl_sse42-merge-diagonals-heap-uint4.o gsnapl_sse42-merge-uint4.o gsnapl_sse42-merge-diagonals-simd-uint4.o gsnapl_sse42-indexdb.o gsnapl_sse42-localdb-read.o gsnapl_sse42-oligo.o gsnapl_sse42-chrnum.o gsnapl_sse42-maxent_hr.o gsnapl_sse42-mapq.o gsnapl_sse42-fopen.o gsnapl_sse42-shortread.o gsnapl_sse42-junction.o gsnapl_sse42-concordance.o gsnapl_sse42-simplepair.o gsnapl_sse42-orderstat.o gsnapl_sse42-intlistpool.o gsnapl_sse42-uintlistpool.o gsnapl_sse42-uint8listpool.o gsnapl_sse42-listpool.o gsnapl_sse42-hitlistpool.o gsnapl_sse42-pathpool.o gsnapl_sse42-auxinfopool.o gsnapl_sse42-pathstorepool.o gsnapl_sse42-intron.o gsnapl_sse42-gbuffer.o gsnapl_sse42-select64-common.o gsnapl_sse42-select64-ones.o gsnapl_sse42-select64-zeroes.o gsnapl_sse42-ef64.o gsnapl_sse42-nr-x.o gsnapl_sse42-knownsplicing.o gsnapl_sse42-knownindels.o gsnapl_sse42-splice.o gsnapl_sse42-indel.o gsnapl_sse42-spliceendsgen.o gsnapl_sse42-spliceends.o gsnapl_sse42-bitpack64-access.o gsnapl_sse42-trdiag.o gsnapl_sse42-trdiagpool.o gsnapl_sse42-tr-extension-search.o gsnapl_sse42-univdiag.o gsnapl_sse42-univdiagpool.o gsnapl_sse42-sedgesort.o gsnapl_sse42-auxinfo.o gsnapl_sse42-pathstore.o gsnapl_sse42-altsplice.o gsnapl_sse42-path.o gsnapl_sse42-pathpair.o gsnapl_sse42-path-solve.o gsnapl_sse42-path-fusion.o gsnapl_sse42-path-trim.o gsnapl_sse42-path-eval.o gsnapl_sse42-pathpair-eval.o gsnapl_sse42-path-print-alignment.o gsnapl_sse42-path-print-m8.o gsnapl_sse42-path-print-sam.o gsnapl_sse42-path-learn.o gsnapl_sse42-method.o gsnapl_sse42-doublelist.o gsnapl_sse42-bitvector.o gsnapl_sse42-transcriptpool.o gsnapl_sse42-exon.o gsnapl_sse42-transcript.o gsnapl_sse42-trpathpool.o gsnapl_sse42-trpath.o gsnapl_sse42-trpath-solve.o gsnapl_sse42-trpath-convert.o gsnapl_sse42-trpath-eval.o gsnapl_sse42-transcriptome-search.o gsnapl_sse42-vectorpool.o gsnapl_sse42-repair.o gsnapl_sse42-transcript-remap.o gsnapl_sse42-transcript-velocity.o gsnapl_sse42-intersect-large.o gsnapl_sse42-intersect-small.o gsnapl_sse42-intersect-uint2.o gsnapl_sse42-intersect-approx-uint4.o gsnapl_sse42-intersect-approx-uint8.o gsnapl_sse42-intersect-approx-indices-uint8.o gsnapl_sse42-intersect-wdups-indices.o gsnapl_sse42-intersect-lower-large.o gsnapl_sse42-intersect-higher-large.o gsnapl_sse42-intersect-indices-small.o gsnapl_sse42-intersect-indices2-large.o gsnapl_sse42-intersect-indices-uint8.o gsnapl_sse42-intersect-concordance-uint8.o gsnapl_sse42-kmer-search.o gsnapl_sse42-extension-search.o gsnapl_sse42-repetitive.o gsnapl_sse42-uint8table.o gsnapl_sse42-stage1hr.o gsnapl_sse42-stage1hr-single.o gsnapl_sse42-stage1hr-paired.o gsnapl_sse42-uint8tableuint.o gsnapl_sse42-tableuint.o gsnapl_sse42-single-cell.o gsnapl_sse42-request.o gsnapl_sse42-resulthr.o gsnapl_sse42-output.o gsnapl_sse42-inbuffer.o gsnapl_sse42-samheader.o gsnapl_sse42-printbuffer.o gsnapl_sse42-outbuffer.o gsnapl_sse42-uint8pairtable.o gsnapl_sse42-splice-count.o gsnapl_sse42-support.o gsnapl_sse42-datadir.o gsnapl_sse42-parserange.o gsnapl_sse42-getline.o gsnapl_sse42-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' @@ -37080,42 +37116,42 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build +chmod +x gmap_process cp gmap_cat.pl gmap_cat +chmod +x gmap_cat +chmod +x gmap_build cp md_coords.pl md_coords cp fa_coords.pl fa_coords +chmod +x md_coords +chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes +chmod +x psl_introns +chmod +x psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites -chmod +x gmap_process -chmod +x gmap_build -chmod +x gmap_cat -chmod +x md_coords -chmod +x fa_coords chmod +x psl_splicesites -chmod +x psl_introns -chmod +x psl_genes -chmod +x ensembl_genes chmod +x gtf_splicesites +chmod +x ensembl_genes cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites -cp gff3_splicesites.pl gff3_splicesites -cp gff3_introns.pl gff3_introns -cp gff3_genes.pl gff3_genes -cp dbsnp_iit.pl dbsnp_iit chmod +x gtf_introns -cp gvf_iit.pl gvf_iit chmod +x gtf_genes +cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites -cp vcf_iit.pl vcf_iit +cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites +cp gff3_genes.pl gff3_genes chmod +x gff3_introns +cp dbsnp_iit.pl dbsnp_iit +cp gvf_iit.pl gvf_iit chmod +x gff3_genes chmod +x dbsnp_iit -chmod +x vcf_iit chmod +x gvf_iit +cp vcf_iit.pl vcf_iit +chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' @@ -37126,7 +37162,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_build --builddir build_avx2 - cd build_avx2 && make -j42 + cd build_avx2 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' @@ -37173,7 +37209,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -37186,7 +37221,6 @@ ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); @@ -37194,31 +37228,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -37235,9 +37248,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -37257,6 +37267,27 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -37282,7 +37313,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -37308,14 +37338,65 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -37347,13 +37428,60 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -37414,10 +37542,20 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -37468,113 +37606,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c @@ -37605,7 +37641,6 @@ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -37619,7 +37654,17 @@ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -37661,6 +37706,17 @@ ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -37673,6 +37729,7 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -37694,8 +37751,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -37704,8 +37759,7 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -37714,8 +37768,10 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read.c: In function 'IIT_read': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -37764,17 +37820,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -37803,7 +37848,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -37824,11 +37868,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -38046,7 +38086,15 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +../../src/indexdb.c: In function 'positions_read_multiple': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -38054,11 +38102,9 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ @@ -38066,6 +38112,7 @@ | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -38076,20 +38123,8 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -38227,16 +38262,12 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -38256,11 +38287,12 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -38281,17 +38313,18 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -38335,14 +38368,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -38382,7 +38411,6 @@ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -38443,6 +38471,115 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -38532,6 +38669,7 @@ | | | long long unsigned int | %lu +../../src/indexdb.c: In function 'positions_read_multiple': ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -38552,6 +38690,9 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -38599,6 +38740,7 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -38651,6 +38793,7 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -38661,119 +38804,26 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ @@ -38787,14 +38837,15 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/compress-write.c: In function 'put_compressed_one': +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -38805,27 +38856,13 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -38853,7 +38890,6 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -38877,9 +38913,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -38900,11 +38933,17 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -38955,9 +38994,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -38967,17 +39003,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/iit_store.c: In function 'parse_fasta': -../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 689 | fprintf(stderr,"Assigning %llu to end\n",end); - | ~~~^ ~~~ - | | | - | | Univcoord_T {aka long unsigned int} - | long long unsigned int - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -38997,8 +39022,14 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c +../../src/iit_store.c: In function 'parse_fasta': +../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 689 | fprintf(stderr,"Assigning %llu to end\n",end); + | ~~~^ ~~~ + | | | + | | Univcoord_T {aka long unsigned int} + | long long unsigned int + | %lu ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -39015,11 +39046,16 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c @@ -39027,6 +39063,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -39077,11 +39115,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -39181,28 +39219,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -39222,15 +39241,34 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/bigendian.c: In function 'Bigendian_write_char': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -39238,6 +39276,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -39328,9 +39367,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -39367,7 +39403,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -39393,9 +39428,12 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -39495,24 +39533,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -39532,10 +39556,43 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -39552,31 +39609,19 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -39590,10 +39635,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -39622,7 +39663,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -39631,6 +39671,7 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -39643,25 +39684,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -39706,19 +39730,135 @@ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -39726,7 +39866,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -39735,8 +39874,6 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -39836,16 +39973,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -39857,13 +39984,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -39952,7 +40072,6 @@ | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -39963,15 +40082,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -39982,16 +40093,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -40054,17 +40155,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -40081,13 +40171,6 @@ | | | long long unsigned int | %lu -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -40098,15 +40181,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -40117,80 +40191,42 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c @@ -40200,30 +40236,22 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -40240,24 +40268,31 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -40283,7 +40318,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -40309,11 +40343,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -40353,7 +40387,6 @@ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -40414,8 +40447,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -40424,14 +40455,14 @@ | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -40440,116 +40471,12 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -40767,6 +40694,112 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -40781,7 +40814,11 @@ | | | | long long unsigned int long unsigned int | %lu +../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -40792,13 +40829,16 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -40810,10 +40850,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -40823,20 +40859,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -40844,10 +40869,6 @@ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); @@ -40859,19 +40880,32 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -40897,7 +40931,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -40923,8 +40956,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -40933,12 +40971,21 @@ | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -41019,8 +41066,6 @@ ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -41033,12 +41078,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -41046,13 +41085,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -41062,16 +41094,6 @@ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -41148,6 +41170,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -41155,12 +41178,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -41168,6 +41185,29 @@ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} +../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -41178,12 +41218,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -41319,10 +41353,6 @@ | | | long long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -41359,7 +41389,6 @@ | | | long long unsigned int | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -41380,6 +41409,13 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ @@ -41414,6 +41450,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -41425,14 +41462,33 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -41453,26 +41509,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c @@ -41506,7 +41542,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -41517,6 +41552,7 @@ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -41534,8 +41570,105 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -41619,44 +41752,12 @@ | ~ | | | Oligospace_T {aka long unsigned int} -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -41677,52 +41778,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': -../../src/iit-read-univ.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -41733,28 +41789,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -41765,8 +41805,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -41777,19 +41815,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -41842,13 +41867,6 @@ | | | long long unsigned int | %lu -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -41869,6 +41887,22 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -41959,6 +41993,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c @@ -41967,6 +42003,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -41981,18 +42019,12 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -42012,7 +42044,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -42033,6 +42064,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c @@ -42088,6 +42124,13 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -42145,6 +42188,7 @@ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -42181,22 +42225,14 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -42304,6 +42340,7 @@ | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -42312,10 +42349,17 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -42327,14 +42371,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c @@ -42374,6 +42410,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -42381,9 +42420,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c @@ -42396,27 +42432,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -42437,7 +42455,25 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -42445,6 +42481,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -42452,6 +42489,7 @@ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -42495,121 +42533,17 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -42617,7 +42551,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -42708,8 +42641,115 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -42732,21 +42772,6 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c @@ -42760,6 +42785,17 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c @@ -42803,6 +42839,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -42811,16 +42854,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -42840,11 +42881,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -42868,6 +42904,9 @@ | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -42918,15 +42957,29 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -43024,23 +43077,11 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -43049,8 +43090,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -43068,7 +43107,6 @@ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -43089,7 +43127,6 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -43150,7 +43187,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c @@ -43165,13 +43201,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c @@ -43200,14 +43236,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c @@ -43222,6 +43250,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c @@ -43269,6 +43305,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -43276,19 +43317,11 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -43309,11 +43342,13 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -43333,13 +43368,15 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -43349,7 +43386,6 @@ 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ @@ -43364,10 +43400,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -43393,6 +43425,7 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -43418,7 +43451,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -43464,7 +43498,6 @@ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -43519,12 +43552,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -43539,8 +43569,8 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -43646,6 +43676,12 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c @@ -43660,15 +43696,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c @@ -43716,31 +43752,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -43768,22 +43779,47 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c @@ -43818,17 +43854,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/stage1hr.c: In function 'Stage1_list_extension': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ @@ -43875,8 +43901,14 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -43884,10 +43916,18 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -43913,30 +43953,9 @@ | | | unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -43956,10 +43975,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -43972,6 +43987,8 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -43980,10 +43997,29 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c @@ -44003,68 +44039,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44164,7 +44138,68 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44173,6 +44208,14 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -44222,7 +44265,7 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -44271,16 +44314,12 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -44292,12 +44331,9 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c @@ -44338,20 +44374,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -44371,6 +44396,17 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44409,109 +44445,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -44562,14 +44495,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44675,9 +44604,114 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -44685,7 +44719,14 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -44697,13 +44738,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44712,6 +44746,8 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c @@ -44719,6 +44755,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -44726,8 +44764,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c @@ -44763,17 +44799,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -44793,6 +44820,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -44813,8 +44843,14 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -44834,9 +44870,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44906,63 +44939,13 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read-univ.c: In function 'read_words': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -44979,7 +44962,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -44987,7 +44969,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -45073,7 +45055,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -45081,7 +45062,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -45089,16 +45069,78 @@ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -45113,21 +45155,15 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c @@ -45158,14 +45194,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -45174,6 +45202,14 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c @@ -45231,12 +45267,38 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -45256,16 +45318,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -45282,36 +45338,16 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c @@ -45336,59 +45372,31 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -45486,6 +45494,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -45502,6 +45511,10 @@ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -45530,6 +45543,24 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -45537,12 +45568,16 @@ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -45571,6 +45606,30 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -45591,30 +45650,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c @@ -45625,6 +45661,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -45632,10 +45672,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c @@ -45659,16 +45695,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -45677,8 +45703,13 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -45687,10 +45718,9 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -45712,23 +45742,15 @@ | ~~~~~~~~~~~~~ | | | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c ../../src/path.c: In function 'Path_print': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ @@ -45749,6 +45771,20 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c @@ -45840,6 +45876,9 @@ gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -45847,37 +45886,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-printbuffer.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-uint8table_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-printbuffer.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genomebits.o gsnap_avx2-genomebits_consec.o gsnap_avx2-genomebits_count.o gsnap_avx2-genomebits_kmer.o gsnap_avx2-genomebits_indel.o gsnap_avx2-genomebits_decode.o gsnap_avx2-genomebits_mismatches.o gsnap_avx2-genomebits_trim.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-mergeinfo.o gsnap_avx2-merge-diagonals-heap-uint4.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-localdb-read.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-junction.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-pathpool.o gsnap_avx2-auxinfopool.o gsnap_avx2-pathstorepool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-select64-common.o gsnap_avx2-select64-ones.o gsnap_avx2-select64-zeroes.o gsnap_avx2-ef64.o gsnap_avx2-nr-x.o gsnap_avx2-knownsplicing.o gsnap_avx2-knownindels.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-spliceendsgen.o gsnap_avx2-spliceends.o gsnap_avx2-bitpack64-access.o gsnap_avx2-trdiag.o gsnap_avx2-trdiagpool.o gsnap_avx2-tr-extension-search.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-auxinfo.o gsnap_avx2-pathstore.o gsnap_avx2-altsplice.o gsnap_avx2-path.o gsnap_avx2-pathpair.o gsnap_avx2-path-solve.o gsnap_avx2-path-fusion.o gsnap_avx2-path-trim.o gsnap_avx2-path-eval.o gsnap_avx2-pathpair-eval.o gsnap_avx2-path-print-alignment.o gsnap_avx2-path-print-m8.o gsnap_avx2-path-print-sam.o gsnap_avx2-path-learn.o gsnap_avx2-method.o gsnap_avx2-doublelist.o gsnap_avx2-bitvector.o gsnap_avx2-transcriptpool.o gsnap_avx2-exon.o gsnap_avx2-transcript.o gsnap_avx2-trpathpool.o gsnap_avx2-trpath.o gsnap_avx2-trpath-solve.o gsnap_avx2-trpath-convert.o gsnap_avx2-trpath-eval.o gsnap_avx2-transcriptome-search.o gsnap_avx2-vectorpool.o gsnap_avx2-repair.o gsnap_avx2-transcript-remap.o gsnap_avx2-transcript-velocity.o gsnap_avx2-intersect-small.o gsnap_avx2-intersect-uint2.o gsnap_avx2-intersect-approx-uint4.o gsnap_avx2-intersect-approx-indices-uint4.o gsnap_avx2-intersect-wdups-indices.o gsnap_avx2-intersect-lower-small.o gsnap_avx2-intersect-higher-small.o gsnap_avx2-intersect-indices-small.o gsnap_avx2-intersect-indices2-small.o gsnap_avx2-intersect-concordance-uint4.o gsnap_avx2-kmer-search.o gsnap_avx2-extension-search.o gsnap_avx2-repetitive.o gsnap_avx2-uint8table.o gsnap_avx2-uinttable.o gsnap_avx2-stage1hr.o gsnap_avx2-stage1hr-single.o gsnap_avx2-stage1hr-paired.o gsnap_avx2-uinttableuint.o gsnap_avx2-tableuint.o gsnap_avx2-single-cell.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-printbuffer.o gsnap_avx2-outbuffer.o gsnap_avx2-uintpairtable.o gsnap_avx2-splice-count.o gsnap_avx2-support.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -45903,6 +45911,34 @@ | | | unsigned int | %lu +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-printbuffer.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-uint8table_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-printbuffer.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genomebits.o gsnap_avx2-genomebits_consec.o gsnap_avx2-genomebits_count.o gsnap_avx2-genomebits_kmer.o gsnap_avx2-genomebits_indel.o gsnap_avx2-genomebits_decode.o gsnap_avx2-genomebits_mismatches.o gsnap_avx2-genomebits_trim.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-mergeinfo.o gsnap_avx2-merge-diagonals-heap-uint4.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-localdb-read.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-junction.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-pathpool.o gsnap_avx2-auxinfopool.o gsnap_avx2-pathstorepool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-select64-common.o gsnap_avx2-select64-ones.o gsnap_avx2-select64-zeroes.o gsnap_avx2-ef64.o gsnap_avx2-nr-x.o gsnap_avx2-knownsplicing.o gsnap_avx2-knownindels.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-spliceendsgen.o gsnap_avx2-spliceends.o gsnap_avx2-bitpack64-access.o gsnap_avx2-trdiag.o gsnap_avx2-trdiagpool.o gsnap_avx2-tr-extension-search.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-auxinfo.o gsnap_avx2-pathstore.o gsnap_avx2-altsplice.o gsnap_avx2-path.o gsnap_avx2-pathpair.o gsnap_avx2-path-solve.o gsnap_avx2-path-fusion.o gsnap_avx2-path-trim.o gsnap_avx2-path-eval.o gsnap_avx2-pathpair-eval.o gsnap_avx2-path-print-alignment.o gsnap_avx2-path-print-m8.o gsnap_avx2-path-print-sam.o gsnap_avx2-path-learn.o gsnap_avx2-method.o gsnap_avx2-doublelist.o gsnap_avx2-bitvector.o gsnap_avx2-transcriptpool.o gsnap_avx2-exon.o gsnap_avx2-transcript.o gsnap_avx2-trpathpool.o gsnap_avx2-trpath.o gsnap_avx2-trpath-solve.o gsnap_avx2-trpath-convert.o gsnap_avx2-trpath-eval.o gsnap_avx2-transcriptome-search.o gsnap_avx2-vectorpool.o gsnap_avx2-repair.o gsnap_avx2-transcript-remap.o gsnap_avx2-transcript-velocity.o gsnap_avx2-intersect-small.o gsnap_avx2-intersect-uint2.o gsnap_avx2-intersect-approx-uint4.o gsnap_avx2-intersect-approx-indices-uint4.o gsnap_avx2-intersect-wdups-indices.o gsnap_avx2-intersect-lower-small.o gsnap_avx2-intersect-higher-small.o gsnap_avx2-intersect-indices-small.o gsnap_avx2-intersect-indices2-small.o gsnap_avx2-intersect-concordance-uint4.o gsnap_avx2-kmer-search.o gsnap_avx2-extension-search.o gsnap_avx2-repetitive.o gsnap_avx2-uint8table.o gsnap_avx2-uinttable.o gsnap_avx2-stage1hr.o gsnap_avx2-stage1hr-single.o gsnap_avx2-stage1hr-paired.o gsnap_avx2-uinttableuint.o gsnap_avx2-tableuint.o gsnap_avx2-single-cell.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-printbuffer.o gsnap_avx2-outbuffer.o gsnap_avx2-uintpairtable.o gsnap_avx2-splice-count.o gsnap_avx2-support.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genomebits.o gsnapl_avx2-genomebits_consec.o gsnapl_avx2-genomebits_count.o gsnapl_avx2-genomebits_kmer.o gsnapl_avx2-genomebits_indel.o gsnapl_avx2-genomebits_decode.o gsnapl_avx2-genomebits_mismatches.o gsnapl_avx2-genomebits_trim.o gsnapl_avx2-dinucl_bits.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-mergeinfo.o gsnapl_avx2-merge-diagonals-heap-uint8.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-diagonals-heap-uint4.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-localdb-read.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-junction.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uintlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-pathpool.o gsnapl_avx2-auxinfopool.o gsnapl_avx2-pathstorepool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-select64-common.o gsnapl_avx2-select64-ones.o gsnapl_avx2-select64-zeroes.o gsnapl_avx2-ef64.o gsnapl_avx2-nr-x.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-knownindels.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-spliceendsgen.o gsnapl_avx2-spliceends.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-trdiag.o gsnapl_avx2-trdiagpool.o gsnapl_avx2-tr-extension-search.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-auxinfo.o gsnapl_avx2-pathstore.o gsnapl_avx2-altsplice.o gsnapl_avx2-path.o gsnapl_avx2-pathpair.o gsnapl_avx2-path-solve.o gsnapl_avx2-path-fusion.o gsnapl_avx2-path-trim.o gsnapl_avx2-path-eval.o gsnapl_avx2-pathpair-eval.o gsnapl_avx2-path-print-alignment.o gsnapl_avx2-path-print-m8.o gsnapl_avx2-path-print-sam.o gsnapl_avx2-path-learn.o gsnapl_avx2-method.o gsnapl_avx2-doublelist.o gsnapl_avx2-bitvector.o gsnapl_avx2-transcriptpool.o gsnapl_avx2-exon.o gsnapl_avx2-transcript.o gsnapl_avx2-trpathpool.o gsnapl_avx2-trpath.o gsnapl_avx2-trpath-solve.o gsnapl_avx2-trpath-convert.o gsnapl_avx2-trpath-eval.o gsnapl_avx2-transcriptome-search.o gsnapl_avx2-vectorpool.o gsnapl_avx2-repair.o gsnapl_avx2-transcript-remap.o gsnapl_avx2-transcript-velocity.o gsnapl_avx2-intersect-large.o gsnapl_avx2-intersect-small.o gsnapl_avx2-intersect-uint2.o gsnapl_avx2-intersect-approx-uint4.o gsnapl_avx2-intersect-approx-uint8.o gsnapl_avx2-intersect-approx-indices-uint8.o gsnapl_avx2-intersect-wdups-indices.o gsnapl_avx2-intersect-lower-large.o gsnapl_avx2-intersect-higher-large.o gsnapl_avx2-intersect-indices-small.o gsnapl_avx2-intersect-indices2-large.o gsnapl_avx2-intersect-indices-uint8.o gsnapl_avx2-intersect-concordance-uint8.o gsnapl_avx2-kmer-search.o gsnapl_avx2-extension-search.o gsnapl_avx2-repetitive.o gsnapl_avx2-uint8table.o gsnapl_avx2-stage1hr.o gsnapl_avx2-stage1hr-single.o gsnapl_avx2-stage1hr-paired.o gsnapl_avx2-uint8tableuint.o gsnapl_avx2-tableuint.o gsnapl_avx2-single-cell.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-printbuffer.o gsnapl_avx2-outbuffer.o gsnapl_avx2-uint8pairtable.o gsnapl_avx2-splice-count.o gsnapl_avx2-support.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' @@ -45910,41 +45946,41 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build +chmod +x gmap_process cp gmap_cat.pl gmap_cat +chmod +x gmap_build +chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords +chmod +x md_coords cp psl_splicesites.pl psl_splicesites -cp psl_introns.pl psl_introns -cp psl_genes.pl psl_genes -chmod +x gmap_process -chmod +x gmap_build -chmod +x gmap_cat -cp ensembl_genes.pl ensembl_genes -cp gtf_splicesites.pl gtf_splicesites chmod +x fa_coords chmod +x psl_splicesites +cp psl_introns.pl psl_introns +cp psl_genes.pl psl_genes chmod +x psl_introns chmod +x psl_genes +cp ensembl_genes.pl ensembl_genes +cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns -chmod +x md_coords cp gtf_genes.pl gtf_genes chmod +x ensembl_genes chmod +x gtf_splicesites +chmod +x gtf_introns +chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites +chmod +x gtf_transcript_splicesites +chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns -chmod +x gtf_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit -chmod +x gtf_genes -cp gvf_iit.pl gvf_iit -chmod +x gtf_transcript_splicesites -cp vcf_iit.pl vcf_iit -chmod +x gff3_splicesites chmod +x gff3_introns chmod +x gff3_genes chmod +x dbsnp_iit +cp gvf_iit.pl gvf_iit chmod +x gvf_iit +cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' Making all in tests @@ -45956,7 +45992,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_build --builddir build_avx512 - cd build_avx512 && make -j42 + cd build_avx512 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' @@ -46003,7 +46039,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -46043,7 +46078,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -46063,26 +46098,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -46108,6 +46128,14 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -46133,16 +46161,19 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -46194,7 +46225,6 @@ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46213,7 +46243,6 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -46237,6 +46266,7 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -46244,8 +46274,61 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -46331,99 +46414,132 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read.c: In function 'IIT_debug': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -46523,20 +46639,72 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -46547,31 +46715,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -46638,13 +46787,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -46661,7 +46803,6 @@ | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -46672,22 +46813,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -46699,38 +46824,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -46741,6 +46840,7 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -46751,7 +46851,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -46762,34 +46861,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -46816,6 +46893,24 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -46826,13 +46921,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -46849,19 +46937,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -46872,53 +46947,10 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -46988,7 +47020,7 @@ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) @@ -47057,6 +47089,10 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -47068,6 +47104,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -47086,16 +47123,15 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ @@ -47115,8 +47151,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -47142,6 +47178,7 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -47166,7 +47203,108 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -47175,7 +47313,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -47253,7 +47390,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -47274,110 +47411,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -47389,7 +47424,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -47406,7 +47440,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -47598,28 +47631,10 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -47634,6 +47649,20 @@ | | | | long long unsigned int long unsigned int | %lu +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -47645,10 +47674,17 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -47660,8 +47696,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -47681,12 +47715,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/indexdb-cat.c: In function 'main': -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ @@ -47699,10 +47728,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ @@ -47710,10 +47735,6 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ @@ -47721,6 +47742,19 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -47729,19 +47763,13 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -47792,14 +47820,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit_store.c: In function 'parse_fasta': -../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 689 | fprintf(stderr,"Assigning %llu to end\n",end); - | ~~~^ ~~~ - | | | - | | Univcoord_T {aka long unsigned int} - | long long unsigned int - | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c @@ -47807,8 +47835,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/iit_store.c: In function 'parse_fasta': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 689 | fprintf(stderr,"Assigning %llu to end\n",end); + | ~~~^ ~~~ + | | | + | | Univcoord_T {aka long unsigned int} + | long long unsigned int + | %lu ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -47828,7 +47863,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -47849,11 +47883,55 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -47878,6 +47956,13 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -47891,6 +47976,7 @@ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -47903,9 +47989,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -47975,7 +48063,7 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -47999,7 +48087,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -48007,11 +48094,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -48020,25 +48104,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -48046,15 +48111,8 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/iit-read.c: In function 'read_tree': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48070,19 +48128,10 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48092,10 +48141,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -48157,20 +48202,9 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -48196,7 +48230,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -48222,9 +48255,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -48258,6 +48296,7 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48301,7 +48340,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -48325,6 +48363,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -48333,7 +48372,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -48341,7 +48379,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -48371,7 +48409,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -48398,6 +48435,7 @@ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48433,32 +48471,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -48478,6 +48492,28 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c @@ -48541,8 +48577,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -48576,6 +48610,7 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48620,6 +48655,7 @@ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48636,13 +48672,14 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/compress-write.c: In function 'put_compressed_one': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ @@ -48650,6 +48687,7 @@ | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ @@ -48773,7 +48811,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -48847,8 +48884,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -48859,12 +48894,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -48891,6 +48920,14 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -48898,6 +48935,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -48911,6 +48949,7 @@ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48940,17 +48979,17 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48975,20 +49014,14 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/iit-read.c: In function 'IIT_debug': +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -49002,6 +49035,12 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -49013,20 +49052,12 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -49038,7 +49069,31 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c @@ -49046,6 +49101,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -49066,31 +49122,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -49141,7 +49175,15 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -49156,8 +49198,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -49166,8 +49206,6 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -49182,6 +49220,7 @@ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -49200,7 +49239,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -49261,31 +49299,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -49296,29 +49309,19 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -49329,19 +49332,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -49362,25 +49352,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -49427,7 +49404,6 @@ | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_annotations': ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -49438,33 +49414,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -49512,19 +49461,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -49545,13 +49487,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -49562,12 +49497,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -49594,9 +49523,18 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -49604,10 +49542,13 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -49615,7 +49556,84 @@ | | | | long long unsigned int long unsigned int | %lu +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -49626,9 +49644,26 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -49640,6 +49675,7 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c @@ -49650,7 +49686,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -49670,6 +49705,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -49690,7 +49727,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -49724,7 +49760,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -49750,10 +49785,18 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -49786,6 +49829,21 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -49824,19 +49882,12 @@ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': -../../src/compress-write.c: In function 'put_compressed_one': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -49854,32 +49905,14 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -49924,7 +49957,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -49986,7 +50018,26 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -49997,6 +50048,16 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -50013,6 +50074,7 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -50033,6 +50095,7 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -50148,7 +50211,6 @@ | | | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -50205,43 +50267,21 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -50253,15 +50293,12 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -50271,7 +50308,6 @@ 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ @@ -50282,7 +50318,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -50303,9 +50338,15 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -50356,15 +50397,219 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -50382,7 +50627,6 @@ | | | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -50584,215 +50828,10 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -50807,9 +50846,6 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -50820,9 +50856,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -50862,11 +50895,19 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -50917,100 +50958,17 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -51079,13 +51037,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -51102,6 +51053,109 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -51115,22 +51169,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51139,7 +51177,8 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -51151,14 +51190,15 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c @@ -51168,10 +51208,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c @@ -51205,6 +51241,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -51212,9 +51251,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -51228,9 +51264,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -51270,62 +51303,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51425,6 +51408,92 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +../../src/compress-write.c: In function 'put_compressed_one': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +../../src/compress-write.c: In function 'Compress_compress': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51489,15 +51558,26 @@ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -51530,56 +51610,16 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -51587,10 +51627,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c @@ -51654,7 +51690,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -51675,7 +51710,6 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -51695,67 +51729,15 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51849,32 +51831,65 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51926,6 +51941,7 @@ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -51960,14 +51976,18 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/iit-read.c: In function 'IIT_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -51981,6 +52001,22 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c @@ -51996,12 +52032,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c @@ -52030,6 +52066,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c @@ -52050,14 +52094,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c @@ -52101,8 +52137,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -52110,9 +52144,10 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -52133,6 +52168,7 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -52144,6 +52180,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -52163,7 +52204,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -52173,6 +52214,7 @@ 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ @@ -52181,19 +52223,10 @@ 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -52220,36 +52253,14 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -52280,6 +52291,15 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -52317,14 +52337,22 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -52453,6 +52481,14 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: @@ -52485,6 +52521,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -52492,12 +52534,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c @@ -52529,6 +52565,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -52537,8 +52575,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c @@ -52546,9 +52582,28 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -52576,30 +52631,14 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -52608,9 +52647,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c @@ -52646,21 +52682,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -52708,6 +52729,28 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -52715,6 +52758,27 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -52740,16 +52804,6 @@ | | | unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -52770,29 +52824,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -52805,7 +52836,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -52814,6 +52844,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c @@ -52836,6 +52872,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -52935,6 +52976,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -52985,7 +53027,21 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -52994,7 +53050,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -53092,23 +53147,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -53120,19 +53159,16 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c @@ -53162,6 +53198,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -53169,8 +53212,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -53190,6 +53231,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -53210,14 +53254,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -53232,22 +53268,124 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -53273,7 +53411,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -53299,7 +53436,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53399,118 +53543,16 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/compress-write.c: In function 'put_compressed_one': -../../src/iit-read.c: In function 'IIT_debug': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -53518,18 +53560,10 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53538,8 +53572,17 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c @@ -53548,13 +53591,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c -../../src/indexdb.c: In function 'positions_read_multiple_large': -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c @@ -53597,13 +53633,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -53650,21 +53679,19 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -53715,16 +53742,25 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -53815,23 +53851,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -53839,7 +53858,13 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -53930,9 +53955,16 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53947,6 +53979,10 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c @@ -53954,12 +53990,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c @@ -53987,6 +54023,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -53995,12 +54037,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c @@ -54054,13 +54090,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -54068,33 +54097,17 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -54114,13 +54127,13 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -54133,12 +54146,35 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c @@ -54155,29 +54191,168 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -54283,166 +54458,27 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c @@ -54454,9 +54490,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -54464,6 +54497,9 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c @@ -54482,6 +54518,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c +../../src/knownindels.c: In function 'Knownindels_new_from_dump': +../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] + 313 | sscanf(line,"%llu %d",&indel_position,&adj) + | ~~~^ ~~~~~~~~~~~~~~~ + | | | + | | Univcoord_T * {aka long unsigned int *} + | long long unsigned int * + | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c @@ -54491,6 +54535,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -54499,21 +54550,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c -../../src/knownindels.c: In function 'Knownindels_new_from_dump': -../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] - 313 | sscanf(line,"%llu %d",&indel_position,&adj) - | ~~~^ ~~~~~~~~~~~~~~~ - | | | - | | Univcoord_T * {aka long unsigned int *} - | long long unsigned int * - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c @@ -54521,7 +54557,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -54549,9 +54584,6 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -54573,6 +54605,10 @@ | ~~~~~~~~~~~~~ | | | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c @@ -54612,10 +54648,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -54663,9 +54695,18 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -54673,21 +54714,36 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx512 gmap_avx512-except.o gmap_avx512-assert.o gmap_avx512-mem.o gmap_avx512-intlist.o gmap_avx512-uintlist.o gmap_avx512-list.o gmap_avx512-littleendian.o gmap_avx512-bigendian.o gmap_avx512-univinterval.o gmap_avx512-interval.o gmap_avx512-stopwatch.o gmap_avx512-semaphore.o gmap_avx512-access.o gmap_avx512-filestring.o gmap_avx512-iit-read-univ.o gmap_avx512-iit-read.o gmap_avx512-md5.o gmap_avx512-bzip2.o gmap_avx512-fopen.o gmap_avx512-sequence.o gmap_avx512-reader.o gmap_avx512-genomicpos.o gmap_avx512-compress.o gmap_avx512-compress-write.o gmap_avx512-gbuffer.o gmap_avx512-genome.o gmap_avx512-popcount.o gmap_avx512-dinucl_bits.o gmap_avx512-genome_canonical.o gmap_avx512-genome-write.o gmap_avx512-bitpack64-read.o gmap_avx512-bitpack64-readtwo.o gmap_avx512-indexdb.o gmap_avx512-oligo.o gmap_avx512-block.o gmap_avx512-chrom.o gmap_avx512-segmentpos.o gmap_avx512-chrnum.o gmap_avx512-uinttable_rh.o gmap_avx512-gregion.o gmap_avx512-match.o gmap_avx512-matchpool.o gmap_avx512-diagnostic.o gmap_avx512-stage1.o gmap_avx512-diag.o gmap_avx512-diagpool.o gmap_avx512-cmet.o gmap_avx512-atoi.o gmap_avx512-orderstat.o gmap_avx512-oligoindex_hr.o gmap_avx512-intron.o gmap_avx512-maxent.o gmap_avx512-maxent_hr.o gmap_avx512-pair.o gmap_avx512-pairpool.o gmap_avx512-cellpool.o gmap_avx512-stage2.o gmap_avx512-doublelist.o gmap_avx512-smooth.o gmap_avx512-splicestringpool.o gmap_avx512-splicetrie_build.o gmap_avx512-splicetrie.o gmap_avx512-boyer-moore.o gmap_avx512-dynprog.o gmap_avx512-dynprog_simd.o gmap_avx512-dynprog_single.o gmap_avx512-dynprog_genome.o gmap_avx512-dynprog_cdna.o gmap_avx512-dynprog_end.o gmap_avx512-translation.o gmap_avx512-pbinom.o gmap_avx512-changepoint.o gmap_avx512-stage3.o gmap_avx512-request.o gmap_avx512-result.o gmap_avx512-output.o gmap_avx512-inbuffer.o gmap_avx512-samheader.o gmap_avx512-printbuffer.o gmap_avx512-outbuffer.o gmap_avx512-chimera.o gmap_avx512-datadir.o gmap_avx512-parserange.o gmap_avx512-getline.o gmap_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx512 gmapl_avx512-except.o gmapl_avx512-assert.o gmapl_avx512-mem.o gmapl_avx512-intlist.o gmapl_avx512-uintlist.o gmapl_avx512-uint8list.o gmapl_avx512-list.o gmapl_avx512-littleendian.o gmapl_avx512-bigendian.o gmapl_avx512-univinterval.o gmapl_avx512-interval.o gmapl_avx512-stopwatch.o gmapl_avx512-semaphore.o gmapl_avx512-access.o gmapl_avx512-filestring.o gmapl_avx512-iit-read-univ.o gmapl_avx512-iit-read.o gmapl_avx512-md5.o gmapl_avx512-bzip2.o gmapl_avx512-fopen.o gmapl_avx512-sequence.o gmapl_avx512-reader.o gmapl_avx512-genomicpos.o gmapl_avx512-compress.o gmapl_avx512-compress-write.o gmapl_avx512-gbuffer.o gmapl_avx512-genome.o gmapl_avx512-popcount.o gmapl_avx512-dinucl_bits.o gmapl_avx512-genome_canonical.o gmapl_avx512-genome-write.o gmapl_avx512-bitpack64-read.o gmapl_avx512-bitpack64-readtwo.o gmapl_avx512-indexdb.o gmapl_avx512-oligo.o gmapl_avx512-block.o gmapl_avx512-chrom.o gmapl_avx512-segmentpos.o gmapl_avx512-chrnum.o gmapl_avx512-uinttable_rh.o gmapl_avx512-uint8table_rh.o gmapl_avx512-gregion.o gmapl_avx512-match.o gmapl_avx512-matchpool.o gmapl_avx512-diagnostic.o gmapl_avx512-stage1.o gmapl_avx512-diag.o gmapl_avx512-diagpool.o gmapl_avx512-cmet.o gmapl_avx512-atoi.o gmapl_avx512-orderstat.o gmapl_avx512-oligoindex_hr.o gmapl_avx512-intron.o gmapl_avx512-maxent.o gmapl_avx512-maxent_hr.o gmapl_avx512-pair.o gmapl_avx512-pairpool.o gmapl_avx512-cellpool.o gmapl_avx512-stage2.o gmapl_avx512-doublelist.o gmapl_avx512-smooth.o gmapl_avx512-splicestringpool.o gmapl_avx512-splicetrie_build.o gmapl_avx512-splicetrie.o gmapl_avx512-boyer-moore.o gmapl_avx512-dynprog.o gmapl_avx512-dynprog_simd.o gmapl_avx512-dynprog_single.o gmapl_avx512-dynprog_genome.o gmapl_avx512-dynprog_cdna.o gmapl_avx512-dynprog_end.o gmapl_avx512-translation.o gmapl_avx512-pbinom.o gmapl_avx512-changepoint.o gmapl_avx512-stage3.o gmapl_avx512-request.o gmapl_avx512-result.o gmapl_avx512-output.o gmapl_avx512-inbuffer.o gmapl_avx512-samheader.o gmapl_avx512-printbuffer.o gmapl_avx512-outbuffer.o gmapl_avx512-chimera.o gmapl_avx512-datadir.o gmapl_avx512-parserange.o gmapl_avx512-getline.o gmapl_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx512 gsnap_avx512-except.o gsnap_avx512-assert.o gsnap_avx512-mem.o gsnap_avx512-intlist.o gsnap_avx512-uintlist.o gsnap_avx512-list.o gsnap_avx512-littleendian.o gsnap_avx512-bigendian.o gsnap_avx512-univinterval.o gsnap_avx512-interval.o gsnap_avx512-stopwatch.o gsnap_avx512-semaphore.o gsnap_avx512-access.o gsnap_avx512-filestring.o gsnap_avx512-iit-read-univ.o gsnap_avx512-iit-read.o gsnap_avx512-bzip2.o gsnap_avx512-reader.o gsnap_avx512-genomicpos.o gsnap_avx512-compress.o gsnap_avx512-genome.o gsnap_avx512-transcriptome.o gsnap_avx512-popcount.o gsnap_avx512-genomebits.o gsnap_avx512-genomebits_consec.o gsnap_avx512-genomebits_count.o gsnap_avx512-genomebits_kmer.o gsnap_avx512-genomebits_indel.o gsnap_avx512-genomebits_decode.o gsnap_avx512-genomebits_mismatches.o gsnap_avx512-genomebits_trim.o gsnap_avx512-dinucl_bits.o gsnap_avx512-genome_sites.o gsnap_avx512-bitpack64-read.o gsnap_avx512-bitpack64-readtwo.o gsnap_avx512-mergeinfo.o gsnap_avx512-merge-diagonals-heap-uint4.o gsnap_avx512-merge-uint4.o gsnap_avx512-merge-diagonals-simd-uint4.o gsnap_avx512-indexdb.o gsnap_avx512-localdb-read.o gsnap_avx512-oligo.o gsnap_avx512-chrnum.o gsnap_avx512-maxent_hr.o gsnap_avx512-mapq.o gsnap_avx512-fopen.o gsnap_avx512-shortread.o gsnap_avx512-junction.o gsnap_avx512-concordance.o gsnap_avx512-simplepair.o gsnap_avx512-orderstat.o gsnap_avx512-intlistpool.o gsnap_avx512-uintlistpool.o gsnap_avx512-listpool.o gsnap_avx512-hitlistpool.o gsnap_avx512-pathpool.o gsnap_avx512-auxinfopool.o gsnap_avx512-pathstorepool.o gsnap_avx512-intron.o gsnap_avx512-gbuffer.o gsnap_avx512-select64-common.o gsnap_avx512-select64-ones.o gsnap_avx512-select64-zeroes.o gsnap_avx512-ef64.o gsnap_avx512-nr-x.o gsnap_avx512-knownsplicing.o gsnap_avx512-knownindels.o gsnap_avx512-splice.o gsnap_avx512-indel.o gsnap_avx512-spliceendsgen.o gsnap_avx512-spliceends.o gsnap_avx512-bitpack64-access.o gsnap_avx512-trdiag.o gsnap_avx512-trdiagpool.o gsnap_avx512-tr-extension-search.o gsnap_avx512-univdiag.o gsnap_avx512-univdiagpool.o gsnap_avx512-sedgesort.o gsnap_avx512-auxinfo.o gsnap_avx512-pathstore.o gsnap_avx512-altsplice.o gsnap_avx512-path.o gsnap_avx512-pathpair.o gsnap_avx512-path-solve.o gsnap_avx512-path-fusion.o gsnap_avx512-path-trim.o gsnap_avx512-path-eval.o gsnap_avx512-pathpair-eval.o gsnap_avx512-path-print-alignment.o gsnap_avx512-path-print-m8.o gsnap_avx512-path-print-sam.o gsnap_avx512-path-learn.o gsnap_avx512-method.o gsnap_avx512-doublelist.o gsnap_avx512-bitvector.o gsnap_avx512-transcriptpool.o gsnap_avx512-exon.o gsnap_avx512-transcript.o gsnap_avx512-trpathpool.o gsnap_avx512-trpath.o gsnap_avx512-trpath-solve.o gsnap_avx512-trpath-convert.o gsnap_avx512-trpath-eval.o gsnap_avx512-transcriptome-search.o gsnap_avx512-vectorpool.o gsnap_avx512-repair.o gsnap_avx512-transcript-remap.o gsnap_avx512-transcript-velocity.o gsnap_avx512-intersect-small.o gsnap_avx512-intersect-uint2.o gsnap_avx512-intersect-approx-uint4.o gsnap_avx512-intersect-approx-indices-uint4.o gsnap_avx512-intersect-wdups-indices.o gsnap_avx512-intersect-lower-small.o gsnap_avx512-intersect-higher-small.o gsnap_avx512-intersect-indices-small.o gsnap_avx512-intersect-indices2-small.o gsnap_avx512-intersect-concordance-uint4.o gsnap_avx512-kmer-search.o gsnap_avx512-extension-search.o gsnap_avx512-repetitive.o gsnap_avx512-uint8table.o gsnap_avx512-uinttable.o gsnap_avx512-stage1hr.o gsnap_avx512-stage1hr-single.o gsnap_avx512-stage1hr-paired.o gsnap_avx512-uinttableuint.o gsnap_avx512-tableuint.o gsnap_avx512-single-cell.o gsnap_avx512-request.o gsnap_avx512-resulthr.o gsnap_avx512-output.o gsnap_avx512-inbuffer.o gsnap_avx512-samheader.o gsnap_avx512-printbuffer.o gsnap_avx512-outbuffer.o gsnap_avx512-uintpairtable.o gsnap_avx512-splice-count.o gsnap_avx512-support.o gsnap_avx512-datadir.o gsnap_avx512-parserange.o gsnap_avx512-getline.o gsnap_avx512-gsnap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -54713,68 +54769,48 @@ | | | unsigned int | %lu -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx512 gsnapl_avx512-except.o gsnapl_avx512-assert.o gsnapl_avx512-mem.o gsnapl_avx512-intlist.o gsnapl_avx512-uintlist.o gsnapl_avx512-uint8list.o gsnapl_avx512-list.o gsnapl_avx512-littleendian.o gsnapl_avx512-bigendian.o gsnapl_avx512-univinterval.o gsnapl_avx512-interval.o gsnapl_avx512-stopwatch.o gsnapl_avx512-semaphore.o gsnapl_avx512-access.o gsnapl_avx512-filestring.o gsnapl_avx512-iit-read-univ.o gsnapl_avx512-iit-read.o gsnapl_avx512-bzip2.o gsnapl_avx512-reader.o gsnapl_avx512-genomicpos.o gsnapl_avx512-compress.o gsnapl_avx512-genome.o gsnapl_avx512-transcriptome.o gsnapl_avx512-popcount.o gsnapl_avx512-genomebits.o gsnapl_avx512-genomebits_consec.o gsnapl_avx512-genomebits_count.o gsnapl_avx512-genomebits_kmer.o gsnapl_avx512-genomebits_indel.o gsnapl_avx512-genomebits_decode.o gsnapl_avx512-genomebits_mismatches.o gsnapl_avx512-genomebits_trim.o gsnapl_avx512-dinucl_bits.o gsnapl_avx512-genome_sites.o gsnapl_avx512-bitpack64-read.o gsnapl_avx512-bitpack64-readtwo.o gsnapl_avx512-mergeinfo.o gsnapl_avx512-merge-diagonals-heap-uint8.o gsnapl_avx512-merge-uint8.o gsnapl_avx512-merge-diagonals-simd-uint8.o gsnapl_avx512-merge-diagonals-heap-uint4.o gsnapl_avx512-merge-uint4.o gsnapl_avx512-merge-diagonals-simd-uint4.o gsnapl_avx512-indexdb.o gsnapl_avx512-localdb-read.o gsnapl_avx512-oligo.o gsnapl_avx512-chrnum.o gsnapl_avx512-maxent_hr.o gsnapl_avx512-mapq.o gsnapl_avx512-fopen.o gsnapl_avx512-shortread.o gsnapl_avx512-junction.o gsnapl_avx512-concordance.o gsnapl_avx512-simplepair.o gsnapl_avx512-orderstat.o gsnapl_avx512-intlistpool.o gsnapl_avx512-uintlistpool.o gsnapl_avx512-uint8listpool.o gsnapl_avx512-listpool.o gsnapl_avx512-hitlistpool.o gsnapl_avx512-pathpool.o gsnapl_avx512-auxinfopool.o gsnapl_avx512-pathstorepool.o gsnapl_avx512-intron.o gsnapl_avx512-gbuffer.o gsnapl_avx512-select64-common.o gsnapl_avx512-select64-ones.o gsnapl_avx512-select64-zeroes.o gsnapl_avx512-ef64.o gsnapl_avx512-nr-x.o gsnapl_avx512-knownsplicing.o gsnapl_avx512-knownindels.o gsnapl_avx512-splice.o gsnapl_avx512-indel.o gsnapl_avx512-spliceendsgen.o gsnapl_avx512-spliceends.o gsnapl_avx512-bitpack64-access.o gsnapl_avx512-trdiag.o gsnapl_avx512-trdiagpool.o gsnapl_avx512-tr-extension-search.o gsnapl_avx512-univdiag.o gsnapl_avx512-univdiagpool.o gsnapl_avx512-sedgesort.o gsnapl_avx512-auxinfo.o gsnapl_avx512-pathstore.o gsnapl_avx512-altsplice.o gsnapl_avx512-path.o gsnapl_avx512-pathpair.o gsnapl_avx512-path-solve.o gsnapl_avx512-path-fusion.o gsnapl_avx512-path-trim.o gsnapl_avx512-path-eval.o gsnapl_avx512-pathpair-eval.o gsnapl_avx512-path-print-alignment.o gsnapl_avx512-path-print-m8.o gsnapl_avx512-path-print-sam.o gsnapl_avx512-path-learn.o gsnapl_avx512-method.o gsnapl_avx512-doublelist.o gsnapl_avx512-bitvector.o gsnapl_avx512-transcriptpool.o gsnapl_avx512-exon.o gsnapl_avx512-transcript.o gsnapl_avx512-trpathpool.o gsnapl_avx512-trpath.o gsnapl_avx512-trpath-solve.o gsnapl_avx512-trpath-convert.o gsnapl_avx512-trpath-eval.o gsnapl_avx512-transcriptome-search.o gsnapl_avx512-vectorpool.o gsnapl_avx512-repair.o gsnapl_avx512-transcript-remap.o gsnapl_avx512-transcript-velocity.o gsnapl_avx512-intersect-large.o gsnapl_avx512-intersect-small.o gsnapl_avx512-intersect-uint2.o gsnapl_avx512-intersect-approx-uint4.o gsnapl_avx512-intersect-approx-uint8.o gsnapl_avx512-intersect-approx-indices-uint8.o gsnapl_avx512-intersect-wdups-indices.o gsnapl_avx512-intersect-lower-large.o gsnapl_avx512-intersect-higher-large.o gsnapl_avx512-intersect-indices-small.o gsnapl_avx512-intersect-indices2-large.o gsnapl_avx512-intersect-indices-uint8.o gsnapl_avx512-intersect-concordance-uint8.o gsnapl_avx512-kmer-search.o gsnapl_avx512-extension-search.o gsnapl_avx512-repetitive.o gsnapl_avx512-uint8table.o gsnapl_avx512-stage1hr.o gsnapl_avx512-stage1hr-single.o gsnapl_avx512-stage1hr-paired.o gsnapl_avx512-uint8tableuint.o gsnapl_avx512-tableuint.o gsnapl_avx512-single-cell.o gsnapl_avx512-request.o gsnapl_avx512-resulthr.o gsnapl_avx512-output.o gsnapl_avx512-inbuffer.o gsnapl_avx512-samheader.o gsnapl_avx512-printbuffer.o gsnapl_avx512-outbuffer.o gsnapl_avx512-uint8pairtable.o gsnapl_avx512-splice-count.o gsnapl_avx512-support.o gsnapl_avx512-datadir.o gsnapl_avx512-parserange.o gsnapl_avx512-getline.o gsnapl_avx512-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' cp gmap_process.pl gmap_process +chmod +x gmap_process cp gmap_build.pl gmap_build +chmod +x gmap_build cp gmap_cat.pl gmap_cat +chmod +x gmap_cat cp md_coords.pl md_coords +chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns -cp psl_genes.pl psl_genes -chmod +x gmap_process -chmod +x gmap_build -cp ensembl_genes.pl ensembl_genes -chmod +x gmap_cat -chmod +x md_coords chmod +x fa_coords chmod +x psl_splicesites +cp psl_genes.pl psl_genes +cp ensembl_genes.pl ensembl_genes chmod +x psl_introns chmod +x psl_genes +chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns -chmod +x ensembl_genes +chmod +x gtf_splicesites +chmod +x gtf_introns cp gtf_genes.pl gtf_genes +chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites +chmod +x gtf_transcript_splicesites +chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns -chmod +x gtf_splicesites -chmod +x gtf_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit -chmod +x gtf_genes cp gvf_iit.pl gvf_iit -chmod +x gtf_transcript_splicesites -chmod +x gff3_splicesites -cp vcf_iit.pl vcf_iit chmod +x gff3_introns chmod +x gff3_genes chmod +x dbsnp_iit chmod +x gvf_iit +cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' Making all in tests @@ -54843,13 +54879,13 @@ /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/reproducible-path/gmap-2024-11-20+ds/build/util/gmap_build |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install --builddir build_avx512 - cd build_avx512 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_avx512 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx512 gmapl.avx512 gsnap.avx512 gsnapl.avx512 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' @@ -54871,18 +54907,18 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' dh_auto_install --builddir build_avx2 - cd build_avx2 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_avx2 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' @@ -54904,12 +54940,12 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_install --builddir build_sse42 - cd build_sse42 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_sse42 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' @@ -54937,18 +54973,18 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_install --builddir build_sse41 - cd build_sse41 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_sse41 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse41 gmapl.sse41 gsnap.sse41 gsnapl.sse41 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' @@ -54970,12 +55006,12 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_install --builddir build_ssse3 - cd build_ssse3 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_ssse3 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' @@ -55003,18 +55039,18 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_install - cd build && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse2 gmapl.sse2 gsnap.sse2 gsnapl.sse2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' @@ -55036,7 +55072,7 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' @@ -55085,8 +55121,8 @@ dh_gencontrol -O--builddir=build dh_md5sums -O--builddir=build dh_builddeb -O--builddir=build -dpkg-deb: building package 'gmap' in '../gmap_2024-11-20+ds-2_amd64.deb'. dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2024-11-20+ds-2_amd64.deb'. +dpkg-deb: building package 'gmap' in '../gmap_2024-11-20+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gmap_2024-11-20+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gmap_2024-11-20+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -55094,12 +55130,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/968878/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/968878/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3100232 and its subdirectories -I: Current time: Sun Sep 27 12:43:21 -12 2026 -I: pbuilder-time-stamp: 1790556201 +I: removing directory /srv/workspace/pbuilder/968878 and its subdirectories +I: Current time: Tue Aug 26 08:40:11 +14 2025 +I: pbuilder-time-stamp: 1756147211